Package: adobeanalyticsr Check: R code for possible problems New result: NOTE aw_workspace_report: no visible binding for global variable ‘id’ make_pretty_segments: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: AHPWR Check: R code for possible problems New result: NOTE flow_chart: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: amanida Check: R code for possible problems New result: NOTE amanida_vote: no visible binding for global variable ‘id’ check_names: no visible binding for global variable ‘id’ compute_amanida: no visible binding for global variable ‘id’ explore_plot: no visible binding for global variable ‘id’ volcano_plot: no visible binding for global variable ‘id’ vote_plot: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: aquacultuR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘digestibility.Rmd’ using rmarkdown Could not fetch http://www.zotero.org/styles/springer-basic-author-date HttpExceptionRequest Request { host = "www.zotero.org" port = 80 secure = False requestHeaders = [] path = "/styles/springer-basic-author-date" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } ResponseTimeout Error: processing vignette 'digestibility.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘digestibility.Rmd’ --- re-building ‘feedconv.Rmd’ using rmarkdown --- finished re-building ‘feedconv.Rmd’ --- re-building ‘growth.Rmd’ using rmarkdown --- finished re-building ‘growth.Rmd’ SUMMARY: processing the following file failed: ‘digestibility.Rmd’ Error: Vignette re-building failed. Execution halted Package: AQuadtree Check: examples New result: ERROR Running examples in ‘AQuadtree-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: AQuadtree-class > ### Title: Class "AQuadtree". > ### Aliases: AQuadtree-class AQuadtree > > ### ** Examples > > data("BarcelonaPop", "BarcelonaCensusTracts") > aquadtree.Barcelona<-AQuadtree(BarcelonaPop, layers = 3) Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. Backtrace: ▆ 1. ├─AQuadtree::AQuadtree(BarcelonaPop, layers = 3) 2. │ └─AQuadtree::createAQuadtree(...) 3. │ └─pts %>% group_by(cellCode) %>% summarise_(.dots = summariseExpr) 4. └─dplyr::summarise_(., .dots = summariseExpr) 5. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: AQuadtree Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘AQuadtreeUse.Rmd’ using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Quitting from AQuadtreeUse.Rmd:96-99 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. i Please use `summarise()` instead. --- Backtrace: x 1. +-AQuadtree::AQuadtree(CharlestonPop) 2. | \-AQuadtree::createAQuadtree(...) 3. | \-pts %>% group_by(cellCode) %>% summarise_(.dots = summariseExpr) 4. \-dplyr::summarise_(., .dots = summariseExpr) 5. \-dplyr:::lazy_defunct("summarise", hint = FALSE) 6. \-lifecycle::deprecate_stop(...) 7. \-lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'AQuadtreeUse.Rmd' failed with diagnostics: `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. --- failed re-building ‘AQuadtreeUse.Rmd’ SUMMARY: processing the following file failed: ‘AQuadtreeUse.Rmd’ Error: Vignette re-building failed. Execution halted Package: assertHE Check: R code for possible problems New result: NOTE find_function_calls_in_folder: no visible binding for global variable ‘location’ processNodes: no visible binding for global variable ‘id’ Undefined global functions or variables: id location Package: auctestr Check: examples New result: ERROR Running examples in ‘auctestr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: auc_compare > ### Title: Compare AUC values using the FBH method. > ### Aliases: auc_compare > > ### ** Examples > > ## load sample experiment data > data(sample_experiment_data) > ## compare VariantA of ModelA and ModelB > auc_compare(sample_experiment_data, + compare_values = c('ModelA', 'ModelB'), + filter_value = c('VariantA'), + time_col = 'time', + outcome_col = 'auc', + compare_col = 'model_id', + over_col = 'dataset', + filter_col = 'model_variant') Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─auctestr::auc_compare(...) 2. │ └─... %>% dplyr::filter_(filter_str) 3. └─dplyr::filter_(., filter_str) 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: auctestr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘basic-auctestr-vignette.Rmd’ using rmarkdown Quitting from basic-auctestr-vignette.Rmd:38-44 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─auctestr::auc_compare(...) 2. │ └─... %>% dplyr::filter_(filter_str) 3. └─dplyr::filter_(., filter_str) 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'basic-auctestr-vignette.Rmd' failed with diagnostics: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘basic-auctestr-vignette.Rmd’ SUMMARY: processing the following file failed: ‘basic-auctestr-vignette.Rmd’ Error: Vignette re-building failed. Execution halted Package: auctestr Check: tests New result: ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(auctestr) > > test_check("auctestr") Saving _problems/test-auc-compare-8.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-auc-compare.R:5:3'): z-score properties are correct ──────────── Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-auc-compare.R:5:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─auctestr::auc_compare(...) 5. │ └─... %>% dplyr::filter_(filter_str) 6. └─dplyr::filter_(., filter_str) 7. └─dplyr:::lazy_defunct("filter") 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ] Error: ! Test failures. Execution halted Package: BaHZING Check: R code for possible problems New result: NOTE Format_BaHZING: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: batchtma Check: examples New result: ERROR Running examples in ‘batchtma-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: adjust_batch > ### Title: Adjust for batch effects > ### Aliases: adjust_batch > > ### ** Examples > > # Data frame with two batches > # Batch 2 has higher values of biomarker and confounder > df <- data.frame( + tma = rep(1:2, times = 10), + biomarker = rep(1:2, times = 10) + + runif(max = 5, n = 20), + confounder = rep(0:1, times = 10) + + runif(max = 10, n = 20) + ) > > # Adjust for batch effects > # Using simple means, ignoring the confounder: > adjust_batch( + data = df, + markers = biomarker, + batch = tma, + method = simple + ) tma biomarker confounder biomarker_adj2 1 1 2.327543 9.3470523 2.916216 2 2 3.860619 3.1214252 3.271947 3 1 3.864267 6.5167377 4.452939 4 2 6.541039 2.2555510 5.952366 5 1 2.008410 2.6722067 2.597082 6 2 6.491948 4.8611409 5.903276 7 1 5.723376 0.1339033 6.312049 8 2 5.303989 4.8238796 4.715316 9 1 4.145570 8.6969085 4.734243 10 2 2.308931 4.4034900 1.720259 11 1 2.029873 4.8208012 2.618546 12 2 2.882784 6.9956583 2.294111 13 1 4.435114 4.9354131 5.023787 14 2 3.920519 2.8621760 3.331846 15 1 4.849207 8.2737332 5.437880 16 2 4.488496 7.6846674 3.899824 17 1 4.588093 7.9423986 5.176765 18 2 6.959530 2.0794363 6.370858 19 1 2.900176 7.2371095 3.488849 20 2 5.887226 5.1127443 5.298553 > # Returns data set with new variable "biomarker_adj2" > > # Use quantile regression, include the confounder, > # change suffix of returned variable: > adjust_batch( + data = df, + markers = biomarker, + batch = tma, + method = quantreg, + confounders = confounder, + suffix = "_batchadjusted" + ) Error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::filter()`: ℹ In argument: `dplyr::across(dplyr::all_of("confounder"), ~!is.na(.x))`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. Backtrace: ▆ 1. ├─batchtma::adjust_batch(...) 2. │ ├─purrr::map(...) 3. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 4. │ │ ├─purrr:::with_indexed_errors(...) 5. │ │ │ └─base::withCallingHandlers(...) 6. │ │ ├─purrr:::call_with_cleanup(...) 7. │ │ └─batchtma (local) .f(.x[[i]], ...) 8. │ │ └─... %>% ... 9. │ └─data %>% ... 10. ├─dplyr::mutate(...) 11. ├─tidyr::nest(., data = dplyr::everything()) 12. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.batchvar)) 13. ├─dplyr::filter(., !is.na(.data$variable)) 14. ├─dplyr::rename(...) 15. ├─dplyr::filter(...) 16. ├─dplyr:::filter.data.frame(...) 17. │ └─dplyr:::filter_impl(...) 18. │ └─dplyr:::filter_rows(...) 19. │ └─dplyr:::filter_eval(...) 20. │ ├─base::withCallingHandlers(...) 21. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 22. │ └─dplyr (local) eval() 23. ├─dplyr:::dplyr_internal_error(...) 24. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 25. │ └─rlang:::signal_abort(cnd, .file) 26. │ └─base::signalCondition(cnd) 27. └─dplyr (local) ``(``) 28. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: batchtma Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘batchtma.Rmd’ using rmarkdown Quitting from batchtma.Rmd:115-120 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::filter()`: ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. --- Backtrace: ▆ 1. ├─... %>% ... 2. ├─batchtma::plot_batch(...) 3. │ ├─dplyr::n_distinct(...) 4. │ │ └─vctrs::df_list(...) 5. │ │ └─rlang::list2(...) 6. │ └─dplyr::select(...) 7. ├─batchtma::adjust_batch(...) 8. │ └─batchtma:::batchmean_ipw(...) 9. │ ├─purrr::map(...) 10. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ │ ├─purrr:::with_indexed_errors(...) 12. │ │ │ └─base::withCallingHandlers(...) 13. │ │ ├─purrr:::call_with_cleanup(...) 14. │ │ └─batchtma (local) .f(.x[[i]], ...) 15. │ │ └─... %>% ... 16. │ └─data %>% ... 17. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.batchvar)) 18. ├─dplyr::filter(., !is.na(.data$variable)) 19. ├─dplyr::rename(., variable = dplyr::one_of(variable)) 20. ├─dplyr::filter(., dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))) 21. ├─dplyr:::filter.data.frame(., dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))) 22. │ └─dplyr:::filter_impl(...) 23. │ └─dplyr:::filter_rows(...) 24. │ └─dplyr:::filter_eval(...) 25. │ ├─base::withCallingHandlers(...) 26. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 27. │ └─dplyr (local) eval() 28. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'batchtma.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `dplyr::filter()`: ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. --- failed re-building ‘batchtma.Rmd’ SUMMARY: processing the following file failed: ‘batchtma.Rmd’ Error: Vignette re-building failed. Execution halted Package: benthos Check: examples New result: ERROR Running examples in ‘benthos-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ambi > ### Title: AZTI Marine Biotic Index (AMBI) > ### Aliases: ambi ambi_ has_ambi has_ambi_ > > ### ** Examples > > ambi( + taxon = c("Euspira pulchella", "Nephtys cirrosa"), + count = c(4, 6) + ) Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─benthos::ambi(...) 2. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group)) 3. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP)) 4. └─dplyr::filter_(., ~!is.na(GROUP)) 5. └─dplyr:::lazy_defunct("filter") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: benthos Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘benthos.Rmd’ using rmarkdown Quitting from benthos.Rmd:664-667 [unnamed-chunk-50] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─d %>% ambi(taxon = TAXON, count = COUNT) 2. ├─benthos::ambi(., taxon = TAXON, count = COUNT) 3. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group)) 4. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP)) 5. └─dplyr::filter_(., ~!is.na(GROUP)) 6. └─dplyr:::lazy_defunct("filter") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'benthos.Rmd' failed with diagnostics: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘benthos.Rmd’ SUMMARY: processing the following file failed: ‘benthos.Rmd’ Error: Vignette re-building failed. Execution halted Package: benthos Check: tests New result: ERROR Running ‘test-all.R’ [3s/3s] Running the tests in ‘tests/test-all.R’ failed. Complete output: > library(testthat) > library(benthos) > test_check("benthos") Saving _problems/test-indicators-208.R Saving _problems/test-indicators-243.R [ FAIL 2 | WARN 0 | SKIP 1 | PASS 139 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-indicators.R:436:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-indicators.R:201:5'): 'AMBI-index' has been correctly implemented ── Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-indicators.R:201:5 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─benthos::ambi(...) 5. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group)) 6. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP)) 7. └─dplyr::filter_(., ~!is.na(GROUP)) 8. └─dplyr:::lazy_defunct("filter") 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('test-indicators.R:236:5'): 'ITI-index' has been correctly implemented ── Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-indicators.R:236:5 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─benthos::iti(...) 5. │ └─benthos::iti_(.data, lazy(taxon), lazy(count), lazy(group)) 6. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP)) 7. └─dplyr::filter_(., ~!is.na(GROUP)) 8. └─dplyr:::lazy_defunct("filter") 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) [ FAIL 2 | WARN 0 | SKIP 1 | PASS 139 ] Error: ! Test failures. Execution halted Package: bistablehistory Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘cumulative-history.Rmd’ using rmarkdown Quitting from cumulative-history.Rmd:67-87 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `summarise()`: ℹ In argument: `t = t`. ℹ In group 1: `h0 = 0`, `S = 1`, `tau = 1`. Caused by error: ! `t` must be size 1, not 100. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─... %>% ... 2. ├─dplyr::summarise(...) 3. ├─dplyr:::summarise.grouped_df(...) 4. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 5. │ └─base::withCallingHandlers(...) 6. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cumulative-history.Rmd' failed with diagnostics: ℹ In argument: `t = t`. ℹ In group 1: `h0 = 0`, `S = 1`, `tau = 1`. Caused by error: ! `t` must be size 1, not 100. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘cumulative-history.Rmd’ --- re-building ‘usage-examples.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. [WARNING] Citeproc: citation loo not found --- finished re-building ‘usage-examples.Rmd’ --- re-building ‘writing-stan-code.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘writing-stan-code.Rmd’ SUMMARY: processing the following file failed: ‘cumulative-history.Rmd’ Error: Vignette re-building failed. Execution halted Package: bistablehistory Check: tests New result: ERROR Running ‘testthat.R’ [10s/10s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(bistablehistory) Loading required package: loo This is loo version 2.9.0 - Online documentation and vignettes at mc-stan.org/loo - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Attaching package: 'loo' The following object is masked from 'package:testthat': compare Loading required package: rlang Loading required package: rstantools This is rstantools version 2.6.0 Attaching package: 'bistablehistory' The following object is masked from 'package:loo': loo > > test_check("bistablehistory") Saving _problems/test-fit_and_post_fit_utilities-44.R [ FAIL 1 | WARN 1 | SKIP 0 | PASS 97 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-fit_and_post_fit_utilities.R:44:3'): test fit and post fit utilities ── Error in `dplyr::summarise(., DistributionParameter = rep(.data$DistributionParameter, dim(bF)[1]), Term = rep(.data$Term, dim(bF)[1]), .groups = "keep")`: ℹ In argument: `DistributionParameter = rep(.data$DistributionParameter, dim(bF)[1])`. ℹ In group 1: `DistributionParameter = 1`, `Term = 1`. Caused by error: ! `DistributionParameter` must be size 1, not 1000. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─testthat::expect_s3_class(fixef(fit), "data.frame") at test-fit_and_post_fit_utilities.R:44:3 2. │ └─testthat::quasi_label(enquo(object)) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─bistablehistory::fixef(fit) 5. │ └─... %>% ... 6. ├─dplyr::mutate(...) 7. ├─dplyr::mutate(...) 8. ├─dplyr::mutate(., Estimate = c(bF)) 9. ├─dplyr::ungroup(.) 10. ├─dplyr::summarise(...) 11. ├─dplyr:::summarise.grouped_df(...) 12. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 13. │ └─base::withCallingHandlers(...) 14. ├─dplyr:::dplyr_internal_error(...) 15. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 16. │ └─rlang:::signal_abort(cnd, .file) 17. │ └─base::signalCondition(cnd) 18. └─dplyr (local) ``(``) 19. └─dplyr (local) handler(cnd) 20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 97 ] Error: ! Test failures. Execution halted Package: bluebike Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘bluebike.Rmd’ using rmarkdown trying URL 'https://s3.amazonaws.com/hubway-data/201501-hubway-tripdata.zip' Quitting from bluebike.Rmd:71-73 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `download.file()`: ! cannot open URL 'https://s3.amazonaws.com/hubway-data/201501-hubway-tripdata.zip' --- Backtrace: ▆ 1. └─bluebike::import_month_data(2015, 1) 2. └─utils::download.file(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bluebike.Rmd' failed with diagnostics: cannot open URL 'https://s3.amazonaws.com/hubway-data/201501-hubway-tripdata.zip' --- failed re-building ‘bluebike.Rmd’ SUMMARY: processing the following file failed: ‘bluebike.Rmd’ Error: Vignette re-building failed. Execution halted Package: bluebike Check: tests New result: ERROR Running ‘testthat.R’ [5s/64s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(bluebike) > > test_check("bluebike") trying URL 'https://s3.amazonaws.com/hubway-data/202002-bluebikes-tripdata.zip' Saving _problems/test-data-27.R [ FAIL 1 | WARN 1 | SKIP 0 | PASS 8 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-data.R:27:3'): imported trip history dataset is a dataframe ──── Error in `download.file(url = str_c("https://s3.amazonaws.com/hubway-data/", ym, "-bluebikes-tripdata.zip"), destfile = str_c(tempdir(), "/", ym, "-hubway-tripdata.zip"))`: cannot open URL 'https://s3.amazonaws.com/hubway-data/202002-bluebikes-tripdata.zip' Backtrace: ▆ 1. └─bluebike::import_month_data(2020, 2) at test-data.R:27:3 2. └─utils::download.file(...) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 8 ] Error: ! Test failures. Execution halted Package: bootnet Check: whether package can be installed New result: ERROR Installation failed. Package: bpmnR Check: R code for possible problems New result: NOTE calculate_CFC: no visible binding for global variable ‘id’ create_xml.bpmn: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: brisk Check: examples New result: ERROR Running examples in ‘brisk-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: benefit > ### Title: Bayesian Benefit Risk > ### Aliases: benefit risk br mcda > > ### ** Examples > > set.seed(1132) > ilogit <- function(x) 1 / (1 + exp(-x)) > out <- mcda( + benefit("CV", function(x) ilogit(x), weight = .75), + risk("DVT", function(x) ilogit(- .5 * x), weight = .25), + br_group( + label = "PBO", + CV = rnorm(1e4, .1), + DVT = rnorm(1e4, .1) + ), + br_group( + label = "TRT", + CV = rnorm(1e4, 2), + DVT = rnorm(1e4, 1) + ) + ) > > out # A tibble: 20,000 × 11 CV CV_weight CV_utility CV_score DVT DVT_weight DVT_utility DVT_score 1 1.47 0.75 0.813 0.610 0.439 0.25 0.445 0.111 2 0.239 0.75 0.559 0.420 -2.12 0.25 0.743 0.186 3 0.969 0.75 0.725 0.544 0.974 0.25 0.381 0.0951 4 0.655 0.75 0.658 0.494 0.0771 0.25 0.490 0.123 5 1.51 0.75 0.819 0.615 -0.993 0.25 0.622 0.155 6 -1.32 0.75 0.210 0.158 -0.874 0.25 0.607 0.152 7 0.395 0.75 0.598 0.448 1.03 0.25 0.375 0.0936 8 -1.43 0.75 0.193 0.145 -0.903 0.25 0.611 0.153 9 0.180 0.75 0.545 0.409 -0.685 0.25 0.585 0.146 10 -0.960 0.75 0.277 0.208 -1.50 0.25 0.679 0.170 # ℹ 19,990 more rows # ℹ 3 more variables: label , iter , total > > summary(out, probs = c(.025, .5, .975)) Error in `dplyr::summarize()`: ℹ In argument: `qtiles = safe_quantile(.data$total, prob = c(0.025, 0.5, 0.975))`. ℹ In group 1: `label = "PBO"`. Caused by error: ! `qtiles` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─base::summary(out, probs = c(0.025, 0.5, 0.975)) 2. ├─brisk:::summary.brisk_br(out, probs = c(0.025, 0.5, 0.975)) 3. │ └─scores %>% dplyr::group_by(.data$label) %>% ... 4. ├─dplyr::summarize(...) 5. ├─dplyr:::summarise.grouped_df(...) 6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 7. │ └─base::withCallingHandlers(...) 8. ├─dplyr:::dplyr_internal_error(...) 9. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 10. │ └─rlang:::signal_abort(cnd, .file) 11. │ └─base::signalCondition(cnd) 12. └─dplyr (local) ``(``) 13. └─dplyr (local) handler(cnd) 14. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: brisk Check: tests New result: ERROR Running ‘testthat.R’ [5s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(brisk) > > test_check("brisk") Saving _problems/test-plot-26.R Saving _problems/test-plot-34.R Saving _problems/test-summary-25.R [ FAIL 3 | WARN 10 | SKIP 4 | PASS 32 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-plot.R:44:3', 'test-plot.R:52:3', 'test-plot.R:60:3', 'test-plot.R:68:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plot.R:26:3'): plot ──────────────────────────────────────────── Error in `dplyr::summarize(., mean = mean(.data$total), qtiles = safe_quantile(.data$total, prob = !!probs))`: i In argument: `qtiles = safe_quantile(.data$total, prob = c(0.025, 0.975))`. i In group 1: `label = "PBO"`. Caused by error: ! `qtiles` must be size 1, not 2. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─base::plot(out) at test-plot.R:26:3 2. ├─brisk:::plot.brisk_br(out) 3. │ ├─base::summary(x, reference = reference) 4. │ └─brisk:::summary.brisk_br(x, reference = reference) 5. │ └─scores %>% dplyr::group_by(.data$label) %>% ... 6. ├─dplyr::summarize(...) 7. ├─dplyr:::summarise.grouped_df(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ └─base::withCallingHandlers(...) 10. ├─dplyr:::dplyr_internal_error(...) 11. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 12. │ └─rlang:::signal_abort(cnd, .file) 13. │ └─base::signalCondition(cnd) 14. └─dplyr (local) ``(``) 15. └─dplyr (local) handler(cnd) 16. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-plot.R:34:3'): plot with ref ─────────────────────────────────── Error in `dplyr::summarize(., mean = mean(.data$total), qtiles = safe_quantile(.data$total, prob = !!probs))`: i In argument: `qtiles = safe_quantile(.data$total, prob = c(0.025, 0.975))`. i In group 1: `label = "TRT"`. Caused by error: ! `qtiles` must be size 1, not 2. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─base::plot(out, reference = "PBO") at test-plot.R:34:3 2. ├─brisk:::plot.brisk_br(out, reference = "PBO") 3. │ ├─base::summary(x, reference = reference) 4. │ └─brisk:::summary.brisk_br(x, reference = reference) 5. │ └─scores %>% dplyr::group_by(.data$label) %>% ... 6. ├─dplyr::summarize(...) 7. ├─dplyr:::summarise.grouped_df(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ └─base::withCallingHandlers(...) 10. ├─dplyr:::dplyr_internal_error(...) 11. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 12. │ └─rlang:::signal_abort(cnd, .file) 13. │ └─base::signalCondition(cnd) 14. └─dplyr (local) ``(``) 15. └─dplyr (local) handler(cnd) 16. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-summary.R:25:3'): summary() ──────────────────────────────────── Error in `dplyr::summarize(., mean = mean(.data$total), qtiles = safe_quantile(.data$total, prob = !!probs))`: i In argument: `qtiles = safe_quantile(.data$total, prob = c(0.025, 0.975))`. i In group 1: `label = "PBO"`. Caused by error: ! `qtiles` must be size 1, not 2. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-summary.R:25:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::summary(res) 5. ├─brisk:::summary.brisk_br(res) 6. │ └─scores %>% dplyr::group_by(.data$label) %>% ... 7. ├─dplyr::summarize(...) 8. ├─dplyr:::summarise.grouped_df(...) 9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 10. │ └─base::withCallingHandlers(...) 11. ├─dplyr:::dplyr_internal_error(...) 12. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 13. │ └─rlang:::signal_abort(cnd, .file) 14. │ └─base::signalCondition(cnd) 15. └─dplyr (local) ``(``) 16. └─dplyr (local) handler(cnd) 17. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 3 | WARN 10 | SKIP 4 | PASS 32 ] Deleting unused snapshots: 'plot/plot-ref.png', 'plot/plot-utility-ref.png', 'plot/plot-utility-stacked-ref.png', 'plot/plot-utility-stacked.png', 'plot/plot-utility.png', and 'plot/plot.png' Error: ! Test failures. Execution halted Package: cardx Check: tests New result: ERROR Running ‘testthat.R’ [321s/181s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("cardx", stop_on_warning = TRUE) Loading required package: cardx Starting 2 test processes. > test-ard_categorical_ci.data.frame.R: 5 missing observations in the "am" column have been removed. > test-ard_effectsize_cohens_d.R: For paired samples, 'repeated_measures_d()' provides more options. > test-ard_effectsize_hedges_g.R: For paired samples, 'repeated_measures_d()' provides more options. Saving _problems/test-ard_missing.survey.design-113.R > test-ard_stats_oneway_test.R: Multiple parameters; naming those columns num.df and den.df. > test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present. > test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present. Saving _problems/test-ard_tabulate.survey.design-1325.R Saving _problems/test-ard_tabulate.survey.design-1343.R Saving _problems/test-ard_tabulate.survey.design-1387.R > test-ard_tabulate_max.R: `AESEV`: "MILD" < "MODERATE" < "SEVERE" Saving _problems/test-ard_tabulate_value.survey.design-799.R Saving _problems/test-ard_total_n.survey.design-15.R Saving _problems/test-ard_total_n.survey.design-37.R [ FAIL 7 | WARN 74 | SKIP 64 | PASS 629 ] ══ Skipped tests (64) ══════════════════════════════════════════════════════════ • On CRAN (64): 'test-ard_attributes.survey.design.R:3:1', 'test-ard_aod_wald_test.R:3:1', 'test-ard_car_vif.R:3:1', 'test-ard_car_vif.R:28:1', 'test-ard_car_anova.R:3:1', 'test-ard_car_anova.R:15:1', 'test-ard_categorical_ci.survey.design.R:6:1', 'test-ard_continuous_ci.survey.design.R:6:1', 'test-ard_continuous_ci.survey.design.R:193:1', 'test-ard_effectsize_cohens_d.R:3:1', 'test-ard_effectsize_hedges_g.R:3:1', 'test-ard_emmeans_emmeans.R:3:1', 'test-ard_emmeans_emmeans.R:93:1', 'test-ard_emmeans_contrast.R:3:1', 'test-ard_emmeans_contrast.R:100:1', 'test-ard_incidence_rate.R:7:1', 'test-ard_incidence_rate.R:43:1', 'test-ard_incidence_rate.R:66:1', 'test-ard_proportion_ci.R:62:1', 'test-ard_proportion_ci.R:112:1', 'test-ard_regression_basic.R:3:1', 'test-ard_regression.R:3:1', 'test-ard_regression.R:40:1', 'test-ard_stats_aov.R:3:1', 'test-ard_stats_kruskal_test.R:3:1', 'test-ard_stats_mantelhaen_test.R:3:1', 'test-ard_stats_mood_test.R:3:1', 'test-ard_stats_oneway_test.R:3:1', 'test-ard_stats_poisson_test.R:73:1', 'test-ard_survey_svychisq.R:3:1', 'test-ard_survey_svyranktest.R:3:1', 'test-ard_survival_survfit.R:3:1', 'test-ard_survival_survfit.R:16:1', 'test-ard_survival_survfit.R:29:1', 'test-ard_survival_survfit.R:42:1', 'test-ard_survival_survfit.R:64:1', 'test-ard_survival_survfit.R:90:1', 'test-ard_survival_survfit.R:120:1', 'test-ard_survival_survfit.R:191:1', 'test-ard_survival_survfit.R:201:1', 'test-ard_survival_survfit.R:221:1', 'test-ard_survival_survfit.R:231:1', 'test-ard_survival_survfit_diff.R:36:1', 'test-ard_tabulate.survey.design.R:421:1', 'test-ard_tabulate.survey.design.R:1176:1', 'test-ard_tabulate.survey.design.R:1410:1', 'test-ard_tabulate_abnormal.R:5:1', 'test-ard_tabulate_abnormal.R:41:1', 'test-ard_tabulate_max.R:1:1', 'test-ard_tabulate_max.R:60:1', 'test-ard_tabulate_max.R:75:1', 'test-ard_tabulate_max.R:115:1', 'test-ard_tabulate_max.R:210:1', 'test-ard_tabulate_max.R:236:1', 'test-ard_tabulate_max.R:258:1', 'test-ard_tabulate_value.survey.design.R:736:1', 'test-ard_total_n.survey.design.R:3:1', 'test-construction_helpers.R:3:1', 'test-construction_helpers.R:103:1', 'test-proportion_ci.R:3:1', 'test-proportion_ci.R:122:1', 'test-ard_summary.survey.design.R:3:1', 'test-ard_summary.survey.design.R:318:1', 'test-ard_summary.survey.design.R:334:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-ard_missing.survey.design.R:110:3'): ard_missing.survey.design() follows ard structure ── Expected `cards::check_ard_structure(...)` to run silently. Actual noise: warnings. ── Failure ('test-ard_tabulate.survey.design.R:1317:3'): ard_tabulate follows ard structure ── Expected `cards::check_ard_structure(...)` to run silently. Actual noise: warnings. ── Failure ('test-ard_tabulate.survey.design.R:1340:3'): ard_tabulate.survey.design() original types are retained ── Expected `... <- NULL` to run silently. Actual noise: warnings. ── Failure ('test-ard_tabulate.survey.design.R:1375:3'): ard_tabulate.survey.design() works with all NA fct variables ── Expected `... <- NULL` to run silently. Actual noise: warnings. ── Failure ('test-ard_tabulate_value.survey.design.R:790:3'): ard_tabulate_value.survey.design() follows ard structure ── Expected `cards::check_ard_structure(...)` to run silently. Actual noise: warnings. ── Failure ('test-ard_total_n.survey.design.R:11:3'): ard_total_n.survey.design() follows ard structure ── Expected `cards::check_ard_structure(...)` to run silently. Actual noise: warnings. ── Failure ('test-ard_total_n.survey.design.R:29:3'): ard_total_n.survey.design() using `update()` ── Expected `ard_total_n(...)` to run silently. Actual noise: warnings. [ FAIL 7 | WARN 74 | SKIP 64 | PASS 629 ] Error: ! Test failures. Execution halted Package: ChinAPIs Check: examples New result: ERROR Running examples in ‘ChinAPIs-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_country_info_cn > ### Title: Get Key Country Information About China from the REST Countries > ### API > ### Aliases: get_country_info_cn > > ### ** Examples > > get_country_info_cn() Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [restcountries.com]: Connection timed out after 10002 milliseconds Calls: get_country_info_cn ... request_fetch.write_memory -> -> raise_libcurl_error Execution halted Package: chunked Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(chunked) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("chunked") Saving _problems/test-verbs-44.R Saving _problems/test-verbs-112.R [ FAIL 3 | WARN 0 | SKIP 1 | PASS 41 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-read.R:6:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-print.R:16:7'): print groups / should print groups chunked info ── Error: The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-print.R:15:5 2. │ └─base::withCallingHandlers(...) 3. ├─testthat::expect_output(print(tbl_iris), "^Source: chunked text file") at test-print.R:16:7 4. │ └─testthat:::quasi_capture(...) 5. │ ├─testthat (local) .capture(...) 6. │ │ └─testthat::capture_output_lines(code, print, width = width) 7. │ │ └─testthat:::eval_with_output(code, print = print, width = width) 8. │ │ ├─withr::with_output_sink(path, withVisible(code)) 9. │ │ │ └─base::force(code) 10. │ │ └─base::withVisible(code) 11. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 12. ├─base::print(tbl_iris) 13. └─chunked:::print.chunkwise(tbl_iris) 14. └─chunked:::head.chunkwise(x) 15. └─x$first_chunk(x$cmds) 16. └─chunked (local) next_chunk(cmds) 17. └─chunked:::play(ch, cmds) 18. └─base::eval(expr, list(.data = .data), enclos = env) 19. └─base::eval(expr, list(.data = .data), enclos = env) 20. ├─dplyr::group_by(.data, Species, add = FALSE) 21. └─dplyr:::group_by.data.frame(.data, Species, add = FALSE) 22. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 23. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 24. └─lifecycle:::deprecate_stop0(msg) 25. └─rlang::cnd_signal(...) ── Error ('test-verbs.R:44:3'): groups() ─────────────────────────────────────── Error: The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─testthat::expect_warning(g <- groups(ir)) at test-verbs.R:44:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dplyr::groups(ir) 7. └─chunked:::groups.chunkwise(ir) 8. ├─dplyr::groups(collect(x, first_chunk_only = TRUE)) 9. ├─dplyr::collect(x, first_chunk_only = TRUE) 10. └─chunked:::collect.chunkwise(x, first_chunk_only = TRUE) 11. └─x$first_chunk(cmds, x$.warn) 12. └─chunked (local) next_chunk(cmds) 13. └─chunked:::play(ch, cmds) 14. └─base::eval(expr, list(.data = .data), enclos = env) 15. └─base::eval(expr, list(.data = .data), enclos = env) 16. ├─dplyr::group_by(.data, Species, add = FALSE) 17. └─dplyr:::group_by.data.frame(.data, Species, add = FALSE) 18. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 19. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 20. └─lifecycle:::deprecate_stop0(msg) 21. └─rlang::cnd_signal(...) ── Error ('test-verbs.R:112:3'): group_by ────────────────────────────────────── Error: The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-verbs.R:112:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─ir %>% summarise(m = mean(Sepal.Width), n = n()) %>% ... 7. ├─base::as.data.frame(.) 8. └─chunked:::as.data.frame.chunkwise(.) 9. ├─base::as.data.frame(...) 10. ├─dplyr::collect(x) 11. └─chunked:::collect.chunkwise(x) 12. └─x$first_chunk(cmds, x$.warn) 13. └─chunked (local) next_chunk(cmds) 14. └─chunked:::play(ch, cmds) 15. └─base::eval(expr, list(.data = .data), enclos = env) 16. └─base::eval(expr, list(.data = .data), enclos = env) 17. ├─dplyr::group_by(.data, Species, add = FALSE) 18. └─dplyr:::group_by.data.frame(.data, Species, add = FALSE) 19. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 20. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 21. └─lifecycle:::deprecate_stop0(msg) 22. └─rlang::cnd_signal(...) [ FAIL 3 | WARN 0 | SKIP 1 | PASS 41 ] Error: ! Test failures. Execution halted Package: CIMPLE Check: R code for possible problems New result: NOTE surv_est: no visible binding for global variable ‘id’ surv_est : coxph_imp: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: cjar Check: R code for possible problems New result: NOTE cja_get_dimensions: no visible binding for global variable ‘id’ cja_get_metrics: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: clinicalomicsdbR Check: examples New result: ERROR Running examples in ‘clinicalomicsdbR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: clinicalomicsdbR > ### Title: clinicalomicsdbR object > ### Aliases: clinicalomicsdbR > > ### ** Examples > > clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$study_list # downloads all files Error in `req_perform()`: ! Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached [trials.linkedomics.org]: Connection timed out after 10001 milliseconds Backtrace: ▆ 1. └─clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab")) 2. └─httr2::req_perform(req, verbosity = self$verbosity) 3. └─httr2:::handle_resp(req, resp, error_call = error_call) 4. └─rlang::cnd_signal(resp) Execution halted Package: cloudos Check: R code for possible problems New result: NOTE .cb_search_phenotypes_v1: no visible binding for global variable ‘id’ .cb_search_phenotypes_v2: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: CLRtools Check: R code for possible problems New result: NOTE cov.patterns: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: cofeatureR Check: tests New result: ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(cofeatureR) > > test_check("cofeatureR") Saving _problems/test_plot_cofeature_mat-23.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_plot_cofeature_mat.R:23:5'): plot_cofeature_mat correctly adds tile borders ── Error: `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. └─cofeatureR::plot_cofeature_mat(in_df, tile.col = cur_border_col) at test_plot_cofeature_mat.R:23:5 2. └─dplyr::mutate_(in.df, .dots = setNames(list(mutate.call), "feature")) 3. └─dplyr:::lazy_defunct("mutate") 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: ! Test failures. Execution halted Package: cohortBuilder Check: tests New result: ERROR Running ‘testthat.R’ [6s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(cohortBuilder) Attaching package: 'cohortBuilder' The following objects are masked from 'package:stats': filter, step > > test_check("cohortBuilder") Saving _problems/test-filter-63.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 270 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-filter.R:63:3'): Multi discrete filter works fine ────────────── Error in `dplyr::filter(., dplyr::across(!!names(values), ~col_in_val(.x, values[[dplyr::cur_column()]], !!keep_na)))`: i In argument: `dplyr::across(...)`. Caused by error: ! `..1` must be a logical vector, not a object. i If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. Backtrace: ▆ 1. ├─coh$run_flow() at test-filter.R:63:3 2. │ └─self$run_step(data_idx) at cohortBuilder/R/cohort_methods.R:633:9 3. │ └─temp_data_object %>% data_filter$filter_data() at cohortBuilder/R/cohort_methods.R:656:9 4. ├─data_filter$filter_data(.) 5. │ └─data_object[[dataset]] %>% ... at cohortBuilder/R/source_tblist.R:587:7 6. ├─dplyr::filter(...) 7. ├─dplyr:::filter.data.frame(...) 8. │ └─dplyr:::filter_impl(...) 9. │ └─dplyr:::filter_rows(...) 10. │ └─dplyr:::filter_eval(...) 11. │ ├─base::withCallingHandlers(...) 12. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 13. │ └─dplyr (local) eval() 14. ├─dplyr:::dplyr_internal_error(...) 15. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 16. │ └─rlang:::signal_abort(cnd, .file) 17. │ └─base::signalCondition(cnd) 18. └─dplyr (local) ``(``) 19. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 270 ] Error: ! Test failures. Execution halted Package: CollapseLevels Check: examples New result: ERROR Running examples in ‘CollapseLevels-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: IVCalc > ### Title: IVCalc > ### Aliases: IVCalc > > ### ** Examples > > > # Load the German_Credit data set supplied with this package > > data("German_Credit") > > l<-list() > > # Call the function as follows > > l<-IVCalc(German_Credit,resp="Good_Bad",bins=10) Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─CollapseLevels::IVCalc(German_Credit, resp = "Good_Bad", bins = 10) 2. │ └─d %>% dplyr::group_by_(naml) %>% dplyr::summarise(tot = dplyr::n()) 3. ├─dplyr::summarise(., tot = dplyr::n()) 4. └─dplyr::group_by_(., naml) 5. └─dplyr:::lazy_defunct("group_by") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: CollapseLevels Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘CollapseLevels.Rmd’ using rmarkdown Quitting from CollapseLevels.Rmd:53-76 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─CollapseLevels::levelsCollapser(...) 2. │ └─d %>% dplyr::group_by_(naml) %>% dplyr::summarise(tot = dplyr::n()) 3. ├─dplyr::summarise(., tot = dplyr::n()) 4. └─dplyr::group_by_(., naml) 5. └─dplyr:::lazy_defunct("group_by") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CollapseLevels.Rmd' failed with diagnostics: `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘CollapseLevels.Rmd’ SUMMARY: processing the following file failed: ‘CollapseLevels.Rmd’ Error: Vignette re-building failed. Execution halted Package: COMIX Check: examples New result: ERROR Running examples in ‘COMIX-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: effectiveSampleSize > ### Title: This function creates an object that summarizes the effective > ### sample size for the parameters of the model. > ### Aliases: effectiveSampleSize > > ### ** Examples > > library(COMIX) > # Number of observations for each sample (row) and cluster (column): > njk <- + matrix( + c( + 150, 300, + 250, 200 + ), + nrow = 2, + byrow = TRUE + ) > > # Dimension of data: > p <- 3 > > # Scale and skew parameters for first cluster: > Sigma1 <- matrix(0.5, nrow = p, ncol = p) + diag(0.5, nrow = p) > alpha1 <- rep(0, p) > alpha1[1] <- -5 > # location parameter for first cluster in first sample: > xi11 <- rep(0, p) > # location parameter for first cluster in second sample (aligned with first): > xi21 <- rep(0, p) > > # Scale and skew parameters for second cluster: > Sigma2 <- matrix(-1/3, nrow = p, ncol = p) + diag(1 + 1/3, nrow = p) > alpha2 <- rep(0, p) > alpha2[2] <- 5 > # location parameter for second cluster in first sample: > xi12 <- rep(3, p) > # location parameter for second cluster in second sample (misaligned with first): > xi22 <- rep(4, p) > > # Sample data: > set.seed(1) > Y <- + rbind( + sn::rmsn(njk[1, 1], xi = xi11, Omega = Sigma1, alpha = alpha1), + sn::rmsn(njk[1, 2], xi = xi12, Omega = Sigma2, alpha = alpha2), + sn::rmsn(njk[2, 1], xi = xi21, Omega = Sigma1, alpha = alpha1), + sn::rmsn(njk[2, 2], xi = xi22, Omega = Sigma2, alpha = alpha2) + ) > > C <- c(rep(1, rowSums(njk)[1]), rep(2, rowSums(njk)[2])) > > prior <- list(zeta = 1, K = 10) > pmc <- list(naprt = 5, nburn = 200, nsave = 200) # Reasonable usage > pmc <- list(naprt = 5, nburn = 2, nsave = 5) # Minimal usage for documentation > # Fit the model: > res <- comix(Y, C, pmc = pmc, prior = prior) initializing all particles... Done > > # Relabel to resolve potential label switching issues: > res_relab <- relabelChain(res) K=10 T=5 N=900 J=2 p=3 > effssz <- effectiveSampleSize(res_relab, "w") Error in `summarize()`: ℹ In argument: `Freq = table(.data$k)/sum(table(.data$k))`. ℹ In group 1: `j = 1`. Caused by error: ! `Freq` must be size 1, not 9. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─COMIX::effectiveSampleSize(res_relab, "w") 2. │ └─COMIX::tidyChain(res, params) 3. │ └─... %>% select(-.data$Freq) 4. ├─dplyr::select(., -.data$Freq) 5. ├─dplyr::mutate(., x = (P + 1)/2, k = names(.data$Freq), frq_t = as.numeric(.data$Freq)) 6. ├─dplyr::summarize(., Freq = table(.data$k)/sum(table(.data$k))) 7. ├─dplyr:::summarise.grouped_df(., Freq = table(.data$k)/sum(table(.data$k))) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ └─base::withCallingHandlers(...) 10. ├─dplyr:::dplyr_internal_error(...) 11. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 12. │ └─rlang:::signal_abort(cnd, .file) 13. │ └─base::signalCondition(cnd) 14. └─dplyr (local) ``(``) 15. └─dplyr (local) handler(cnd) 16. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: contentanalysis Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘introduction.Rmd’ using rmarkdown trying URL 'https://raw.githubusercontent.com/massimoaria/contentanalysis/master/inst/examples/example_paper.pdf' Content type 'application/octet-stream' length 543702 bytes (530 KB) ================================================== downloaded 530 KB Quitting from introduction.Rmd:216-223 [reference-sources] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `analysis$parsed_references[, c("ref_first_author", "ref_year", "ref_journal", "ref_source")]`: ! Can't subset columns that don't exist. ✖ Column `ref_journal` doesn't exist. --- Backtrace: ▆ 1. ├─utils::head(...) 2. ├─...[] 3. └─tibble:::`[.tbl_df`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'introduction.Rmd' failed with diagnostics: Can't subset columns that don't exist. ✖ Column `ref_journal` doesn't exist. --- failed re-building ‘introduction.Rmd’ SUMMARY: processing the following file failed: ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: crawl Check: R code for possible problems New result: NOTE crw_as_sf.list : make_mls: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: crosswalkr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘collapse.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘collapse.Rmd’ --- re-building ‘crosswalkr.Rmd’ using rmarkdown Quitting from crosswalkr.Rmd:198-204 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- Backtrace: ▆ 1. ├─file_1 %>% tbl_df() 2. └─dplyr::tbl_df(.) 3. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 4. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'crosswalkr.Rmd' failed with diagnostics: `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- failed re-building ‘crosswalkr.Rmd’ SUMMARY: processing the following file failed: ‘crosswalkr.Rmd’ Error: Vignette re-building failed. Execution halted Package: dataCompareR Check: examples New result: ERROR Running examples in ‘dataCompareR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: print.dataCompareRobject > ### Title: Printing RCompare Output > ### Aliases: print.dataCompareRobject > > ### ** Examples > > rc1 <- rCompare(iris,iris) Running rCompare... Error: ! `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) Execution halted Package: dataCompareR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘dataCompareR.Rmd’ using rmarkdown Quitting from dataCompareR.Rmd:60-63 [runcomp] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. --- Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris2) 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'dataCompareR.Rmd' failed with diagnostics: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. --- failed re-building ‘dataCompareR.Rmd’ SUMMARY: processing the following file failed: ‘dataCompareR.Rmd’ Error: Vignette re-building failed. Execution halted Package: dataCompareR Check: tests New result: ERROR Running ‘testthat.R’ [11s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # SPDX-Copyright: Copyright (c) Capital One Services, LLC > # SPDX-License-Identifier: Apache-2.0 > # Copyright 2017 Capital One Services, LLC > # > # Licensed under the Apache License, Version 2.0 (the "License"); > # you may not use this file except in compliance with the License. > # > # You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 > # > # Unless required by applicable law or agreed to in writing, software distributed > # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS > # OF ANY KIND, either express or implied. > > # This appears to be required to use covr for package coverage > > library(testthat) > library(dataCompareR) > > test_check("dataCompareR") Saving _problems/testCheckPrintObject-38.R Saving _problems/testCheckPrintObject-62.R Saving _problems/testCheckPrintObject-121.R Saving _problems/testCheckPrintObject-167.R Saving _problems/testCheckPrintObject-188.R Saving _problems/testCheckPrintObject-212.R Saving _problems/testCheckPrintObject-261.R Saving _problems/testCheckSummaryObject-41.R Saving _problems/testCheckSummaryObject-71.R Saving _problems/testCheckSummaryObject-157.R Saving _problems/testCheckisRCompareObject-33.R Saving _problems/testCompareDifferentDFs-26.R Saving _problems/testCreateCompareObject-28.R Saving _problems/testCreateMismatchData-49.R Saving _problems/testCreateMismatchData-61.R Saving _problems/testCreateMismatchData-92.R Saving _problems/testCreateMismatchData-106.R Saving _problems/testCreateMismatchData-131.R Saving _problems/testCreateMismatchData-166.R Saving _problems/testCreateMismatchObject-68.R Saving _problems/testEndToEnd1ColFrames-32.R Saving _problems/testEndToEnd1ColFrames-76.R Saving _problems/testEndToEndBit64-39.R Saving _problems/testEndToEndDates-35.R Saving _problems/testEndToEndDates-58.R Saving _problems/testEndToEndDates-79.R Saving _problems/testEndToEndFourKeys-35.R Saving _problems/testEndToEndFourKeys-77.R Saving _problems/testEndToEndFourKeys-119.R Saving _problems/testEndToEndFourKeys-160.R Saving _problems/testEndToEndMismatchParam-42.R Saving _problems/testEndToEndMismatchParam-43.R Saving _problems/testEndToEndOrderedFactors-34.R Saving _problems/testEndToEndTimes-35.R Saving _problems/testEndToEndTitanic-35.R Saving _problems/testEndToEndTitanic-111.R Saving _problems/testEndToEndTitanic-253.R Saving _problems/testEndToEndTitanic-307.R Saving _problems/testEndToEndTitanic-339.R Saving _problems/testEndToEndTitanic-347.R Saving _problems/testEndToEndTitanic-350.R Saving _problems/testEndToEndTwoKeys-35.R Saving _problems/testEndToEndTwoKeys-73.R Saving _problems/testEndToEndTwoKeys-111.R Saving _problems/testEndToEndTwoKeys-148.R Saving _problems/testLocateMismatches-44.R Saving _problems/testLocateMismatches-67.R Saving _problems/testLocateMismatches-91.R Saving _problems/testLocateMismatches-108.R Saving _problems/testMakeValidNames-100.R Saving _problems/testMakeValidNames-145.R Saving _problems/testMatchColumns-66.R Saving _problems/testMatchMultiIndex-91.R Saving _problems/testMatchRows-104.R Saving _problems/testMatchSingleIndex-42.R Saving _problems/testPrintSummaryRcompareObject-32.R Saving _problems/testPrintSummaryRcompareObject-92.R Saving _problems/testPrintSummaryRcompareObject-118.R Saving _problems/testPrintSummaryRcompareObject-138.R Saving _problems/testPrintSummaryRcompareObject-193.R Saving _problems/testPrintSummaryRcompareObject-239.R Saving _problems/testRCompareStructure-37.R Saving _problems/testRCompareStructure-71.R Saving _problems/testRCompareStructure-123.R Saving _problems/testcreateReportText-30.R Saving _problems/testcreateReportText-94.R Saving _problems/testcreateReportText-118.R Saving _problems/testcreateReportText-138.R Saving _problems/testcreateReportText-158.R [ FAIL 70 | WARN 0 | SKIP 3 | PASS 180 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'testSaveReport.R:28:3', 'testSaveReport.R:70:3', 'testSaveReport.R:94:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('testCheckPrintObject.R:38:5'): print only generates message when data sets match ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic2, titanic2) at testCheckPrintObject.R:38:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckPrintObject.R:62:5'): print returns message and data when mismatches occur ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testCheckPrintObject.R:62:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckPrintObject.R:121:3'): print rcomp object ────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) at testCheckPrintObject.R:121:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckPrintObject.R:167:3'): test print rcompobj rows columns dropped messages ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure, pressure) at testCheckPrintObject.R:167:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckPrintObject.R:188:3'): test print argument validation ────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) at testCheckPrintObject.R:188:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckPrintObject.R:212:3'): test print with two empty data frames ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df_empty, df_empty) at testCheckPrintObject.R:212:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckPrintObject.R:261:3'): test print with one empty data frames ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df_empty, df_not_empty) at testCheckPrintObject.R:261:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckSummaryObject.R:41:5'): compareSummaryEqual ──────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic2, titanic2) at testCheckSummaryObject.R:41:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckSummaryObject.R:71:5'): compareSummaryUnEqual ────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testCheckSummaryObject.R:71:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckSummaryObject.R:157:5'): summary errors if incorrect args passed ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testCheckSummaryObject.R:157:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCheckisRCompareObject.R:33:5'): isdataCompareRobject ──────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic2, titanic2) at testCheckisRCompareObject.R:33:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCompareDifferentDFs.R:26:3'): check two dfs with no overlap ───── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_message(rCompare(iris, women), "Running rCompare") at testCompareDifferentDFs.R:26:3 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(iris, women) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Error ('testCreateCompareObject.R:28:3'): compareObject ───────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) at testCreateCompareObject.R:28:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchData.R:49:5'): noMismatches ─────────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic2, titanic2) at testCreateMismatchData.R:49:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchData.R:61:5'): Mismatches ───────────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic, titanic2) at testCreateMismatchData.R:61:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchData.R:92:5'): No data ──────────────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic, titanic2) at testCreateMismatchData.R:92:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchData.R:106:3'): With match key ──────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure, pressure2, keys = "temperature") at testCreateMismatchData.R:106:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchData.R:131:3'): With two match keys ─────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testCreateMismatchData.R:131:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchData.R:166:3'): With lists and matrices ─────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(mat, mat2) at testCreateMismatchData.R:166:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testCreateMismatchObject.R:64:3'): Mismatches work ────────────────── Error: `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. Backtrace: ▆ 1. ├─base::unlist(...) at testCreateMismatchObject.R:64:3 2. ├─... %>% summarize_each(anyNegative) 3. └─dplyr::summarize_each(., anyNegative) 4. └─dplyr:::each_defunct("summarise_each()") 5. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()") 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('testEndToEnd1ColFrames.R:32:3'): Comparison with missing row ──────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df1, df2) at testEndToEnd1ColFrames.R:32:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEnd1ColFrames.R:76:3'): Comparison with equal datasets ───── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df1, df2) at testEndToEnd1ColFrames.R:76:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndBit64.R:39:5'): ComparisonOfBit64Fields ───────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(dfTableA, dfTableB, keys = c("color")) at testEndToEndBit64.R:39:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndDates.R:35:3'): ComparisonOfEqualDates ────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(dfTableA, dfTableB, keys = c("color")) at testEndToEndDates.R:35:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndDates.R:58:3'): ComparisonOfPOSIXDates ────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(dfTableA, dfTableB, keys = c("color")) at testEndToEndDates.R:58:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndDates.R:79:3'): ComparisonOfMixedDates ────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(dfTableA, dfTableB, keys = c("color")) at testEndToEndDates.R:79:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndFourKeys.R:35:3'): ComparisonOfEquals ─────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndFourKeys.R:35:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndFourKeys.R:77:3'): ComparisonOfUnEquals ───────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndFourKeys.R:77:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndFourKeys.R:119:3'): ComparisonOfMissRows ──────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndFourKeys.R:119:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndFourKeys.R:160:3'): ComparisonOfMissCols ──────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndFourKeys.R:160:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Failure ('testEndToEndMismatchParam.R:42:3'): Mismatch stops when exceeded ── `rCompare(iris, iris2, mismatches = 20)` threw an error. Message: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Class: lifecycle_error_deprecated/defunctError/rlang_error/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at testEndToEndMismatchParam.R:42:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(iris, iris2, mismatches = 20) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Failure ('testEndToEndMismatchParam.R:43:3'): Mismatch stops when exceeded ── `rCompare(iris, iris2, mismatches = 21)` threw an error. Message: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Class: lifecycle_error_deprecated/defunctError/rlang_error/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at testEndToEndMismatchParam.R:43:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(iris, iris2, mismatches = 21) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Error ('testEndToEndOrderedFactors.R:34:3'): ComparisonOfOrderedFactor ────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(dfTableA, dfTableB, keys = c("color")) at testEndToEndOrderedFactors.R:34:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTimes.R:35:3'): ComparisonOfEqualDates ────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(dfTableA, dfTableB, keys = c("color")) at testEndToEndTimes.R:35:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTitanic.R:35:5'): ComparisonOfEquals ──────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic2, titanic2, trimChars = TRUE) at testEndToEndTitanic.R:35:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTitanic.R:111:5'): ComparisonOfUnequals ───────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndTitanic.R:111:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTitanic.R:253:5'): ComparisonWithMissingRows ──────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(titanic, titanic3, trimChars = TRUE, keys = "PassengerId") at testEndToEndTitanic.R:253:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTitanic.R:307:5'): ComparisonWithMissingCols ──────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndTitanic.R:307:5 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Failure ('testEndToEndTitanic.R:339:7'): TestRoundingEndToEnd ─────────────── `... <- NULL` threw an error. Message: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Class: lifecycle_error_deprecated/defunctError/rlang_error/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at testEndToEndTitanic.R:339:7 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(...) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Failure ('testEndToEndTitanic.R:347:7'): TestRoundingEndToEnd ─────────────── `... <- NULL` threw an error. Message: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Class: lifecycle_error_deprecated/defunctError/rlang_error/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at testEndToEndTitanic.R:347:7 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(...) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Error ('testEndToEndTitanic.R:350:7'): TestRoundingEndToEnd ───────────────── Error in `eval(code, test_env)`: object 'roundedCompare2' not found Backtrace: ▆ 1. ├─testthat::expect_true(...) at testEndToEndTitanic.R:350:7 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::nrow(roundedCompare2$mismatches$AGE) ── Error ('testEndToEndTwoKeys.R:35:3'): ComparisonOfEquals ──────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndTwoKeys.R:35:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTwoKeys.R:73:3'): ComparisonOfUnEquals ────────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndTwoKeys.R:73:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTwoKeys.R:111:3'): ComparisonOfMissRows ───────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndTwoKeys.R:111:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testEndToEndTwoKeys.R:148:3'): ComparisonOfMissCols ───────────────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testEndToEndTwoKeys.R:148:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testLocateMismatches.R:44:3'): locateMismatches with a single key ─── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at testLocateMismatches.R:44:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─dataCompareR:::locateMismatches(DFA, DFA, keys = "k") 5. ├─base::sapply(select_(DFA, .dots = colCompare), collapseClasses) 6. │ └─base::lapply(X = X, FUN = FUN, ...) 7. └─dplyr::select_(DFA, .dots = colCompare) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testLocateMismatches.R:67:3'): locateMismatches with multiple keys ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at testLocateMismatches.R:67:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─dataCompareR:::locateMismatches(DFA, DFA, keys = c("k1", "k2")) 5. ├─base::sapply(select_(DFA, .dots = colCompare), collapseClasses) 6. │ └─base::lapply(X = X, FUN = FUN, ...) 7. └─dplyr::select_(DFA, .dots = colCompare) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testLocateMismatches.R:91:3'): locateMismatches handling NAs ──────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at testLocateMismatches.R:91:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─dataCompareR:::locateMismatches(DFA, DFB, keys = "k") 5. ├─base::sapply(select_(DFA, .dots = colCompare), collapseClasses) 6. │ └─base::lapply(X = X, FUN = FUN, ...) 7. └─dplyr::select_(DFA, .dots = colCompare) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testLocateMismatches.R:108:3'): locateMismatches with no key information ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at testLocateMismatches.R:108:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─dataCompareR:::locateMismatches(DFA, DFA, keys = NULL) 5. ├─base::sapply(select_(DFA, .dots = colCompare), collapseClasses) 6. │ └─base::lapply(X = X, FUN = FUN, ...) 7. └─dplyr::select_(DFA, .dots = colCompare) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testMakeValidNames.R:100:3'): makeValidNames function in end to end context ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_message(a <- rCompare(iris, iris2), "Fixing syntactically invalid names") at testMakeValidNames.R:100:3 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(iris, iris2) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Error ('testMakeValidNames.R:145:3'): makeValidKeys function in end to end context ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_message(rCompare(aa, bb)) at testMakeValidNames.R:145:3 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─dataCompareR::rCompare(aa, bb) 7. │ └─dataCompareR:::processFlow(...) 8. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 9. │ └─dataCompareR:::matchColumns(dfA, dfB) 10. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 11. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 12. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 13. └─dplyr:::lazy_defunct("select", hint = FALSE) 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) ── Error ('testMatchColumns.R:66:3'): function passes overall functionality ──── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(matchColumns(inDfa, inDfb), result) at testMatchColumns.R:66:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─dataCompareR:::matchColumns(inDfa, inDfb) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testMatchMultiIndex.R:91:3'): matchMultiIndex doesn't produce any warnings when creating output ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(...) at testMatchMultiIndex.R:91:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testMatchRows.R:104:3'): matchRows correctly finds matching rows ──── Error: `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─dataCompareR:::matchRows(df1, df2, "ky") at testMatchRows.R:104:3 2. │ └─dataCompareR:::matchSingleIndex(df_a, df_b, indices) 3. │ └─df_a[df_a[, index_key] %in% index_subset, ] %>% ... 4. └─dplyr::arrange_(., index_key) 5. └─dplyr:::lazy_defunct("arrange") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) ── Error ('testMatchSingleIndex.R:42:3'): matchSingleIndex correctly finds matching rows ── Error: `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─dataCompareR:::matchSingleIndex(df1, df2, "ky") at testMatchSingleIndex.R:42:3 2. │ └─df_a[df_a[, index_key] %in% index_subset, ] %>% ... 3. └─dplyr::arrange_(., index_key) 4. └─dplyr:::lazy_defunct("arrange") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:32:3'): test printsummaryrcompobj ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) at testPrintSummaryRcompareObject.R:32:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:92:3'): rounding note appears ────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris, roundDigits = 0) at testPrintSummaryRcompareObject.R:92:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:118:3'): complete mismatching data output is truncated ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, pressure) at testPrintSummaryRcompareObject.R:118:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:138:3'): row matching details appear only when matching on keys and row matching is incomplete ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) at testPrintSummaryRcompareObject.R:138:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:170:3'): the number of rows and columns returned are correct ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─utils::capture.output(print(rCompare(pressure2, pressure2, keys = c("temperature")))) at testPrintSummaryRcompareObject.R:170:3 2. │ └─base::withVisible(...elt(i)) 3. ├─base::print(rCompare(pressure2, pressure2, keys = c("temperature"))) 4. ├─dataCompareR::rCompare(pressure2, pressure2, keys = c("temperature")) 5. │ └─dataCompareR:::processFlow(...) 6. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 7. │ └─dataCompareR:::matchColumns(dfA, dfB) 8. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 9. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 10. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 11. └─dplyr:::lazy_defunct("select", hint = FALSE) 12. └─lifecycle::deprecate_stop(...) 13. └─lifecycle:::deprecate_stop0(msg) 14. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:193:3'): the output is correct when both dataframes have no rows ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df_empty, df_empty) at testPrintSummaryRcompareObject.R:193:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testPrintSummaryRcompareObject.R:239:3'): the output is correct when one dataframes has no columns ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df_empty, df_not_empty) at testPrintSummaryRcompareObject.R:239:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testRCompareStructure.R:37:3'): dataCompareR object meets requirements in row matching ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure2, pressure, keys = "temperature") at testRCompareStructure.R:37:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testRCompareStructure.R:71:3'): dataCompareR object when both datasets have no rows ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df_empty, df_empty) at testRCompareStructure.R:71:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testRCompareStructure.R:123:3'): dataCompareR object when one datasets has no rows ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(df_empty, df_not_empty) at testRCompareStructure.R:123:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testcreateReportText.R:30:3'): check a non comprehensive set of properties about createReportText ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(iris, iris) at testcreateReportText.R:30:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testcreateReportText.R:94:3'): check a key based match with 1 matching keys ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure, pressure2) at testcreateReportText.R:94:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testcreateReportText.R:118:3'): check that the max difference works with negative values ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure, pressure2) at testcreateReportText.R:118:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testcreateReportText.R:138:3'): checkthe column headers in tables contain the right data ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure, pressure2) at testcreateReportText.R:138:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('testcreateReportText.R:158:3'): test that keys vs no keys has the correct output in the mismatch table ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─dataCompareR::rCompare(pressure, pressure2) at testcreateReportText.R:158:3 2. │ └─dataCompareR:::processFlow(...) 3. │ └─dataCompareR:::prepareData(dfa, dfb, keys, trimChars) 4. │ └─dataCompareR:::matchColumns(dfA, dfB) 5. │ └─dataCompareR:::subsetDataColumns(DFA, DFB, colInfoList) 6. │ └─DFA %>% select_(.dots = colInfoList[["commonCols"]]) 7. └─dplyr::select_(., .dots = colInfoList[["commonCols"]]) 8. └─dplyr:::lazy_defunct("select", hint = FALSE) 9. └─lifecycle::deprecate_stop(...) 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) [ FAIL 70 | WARN 0 | SKIP 3 | PASS 180 ] Error: ! Test failures. Execution halted Package: dbplot Check: examples New result: ERROR Running examples in ‘dbplot-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: db_compute_boxplot > ### Title: Returns a dataframe with boxplot calculations > ### Aliases: db_compute_boxplot > > ### ** Examples > > > mtcars %>% + db_compute_boxplot(am, mpg) Error: ! The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─mtcars %>% db_compute_boxplot(am, mpg) 2. └─dbplot::db_compute_boxplot(., am, mpg) 3. ├─dplyr::group_by(data, !!!x, add = TRUE) 4. └─dplyr:::group_by.data.frame(data, !!!x, add = TRUE) 5. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 6. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: dbplot Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(dbplot) > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(ggplot2) > > test_check("dbplot") Saving _problems/test-boxplots-4.R Saving _problems/test-boxplots-8.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-boxplots.R:4:3'): dbplot_boxplot() returns a ggplot ──────────── Error: The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─testthat::expect_is(dbplot_boxplot(mtcars, am, mpg), "ggplot") at test-boxplots.R:4:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─dbplot:::dbplot_boxplot(mtcars, am, mpg) 5. └─dbplot::db_compute_boxplot(...) 6. ├─dplyr::group_by(data, !!!x, add = TRUE) 7. └─dplyr:::group_by.data.frame(data, !!!x, add = TRUE) 8. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 9. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('test-boxplots.R:8:3'): db_compute_boxplot() returns the right number of rows ── Error: The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-boxplots.R:8:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(db_compute_boxplot(mtcars, am, mpg)) 5. └─dbplot::db_compute_boxplot(mtcars, am, mpg) 6. ├─dplyr::group_by(data, !!!x, add = TRUE) 7. └─dplyr:::group_by.data.frame(data, !!!x, add = TRUE) 8. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 9. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ] Error: ! Test failures. Execution halted Package: dbplyr Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'nycflights13.Rd': ‘[dplyr:src_dbi]{dplyr::src_postgres()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: delimtools Check: examples New result: ERROR Running examples in ‘delimtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: match_ratio > ### Title: Compute Agreement Between Alternative Species Delimitation > ### Partitions > ### Aliases: match_ratio > > ### ** Examples > > > # estimate match ratio statistics > match_ratio(geophagus_delims) Error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::mutate()`: ℹ In argument: `n_match = dplyr::if_else(dplyr::pick(2) == dplyr::pick(3), union, 0)`. Caused by error in `dplyr::if_else()`: ! `condition` must be a logical vector, not a logical matrix. Backtrace: ▆ 1. ├─delimtools::match_ratio(geophagus_delims) 2. │ ├─dplyr::ungroup(...) 3. │ ├─dplyr::arrange(...) 4. │ ├─dplyr::group_by(...) 5. │ ├─purrr::list_rbind(...) 6. │ │ └─purrr:::check_list_of_data_frames(x) 7. │ │ └─vctrs::obj_check_list(x, call = error_call) 8. │ ├─rlang::set_names(...) 9. │ └─purrr::map(...) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─delimtools (local) .f(.x[[i]], ...) 15. │ ├─dplyr::summarise(...) 16. │ ├─dplyr::mutate(...) 17. │ └─dplyr:::mutate.data.frame(...) 18. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 19. │ ├─base::withCallingHandlers(...) 20. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 21. │ └─mask$eval_all_mutate(quo) 22. │ └─dplyr (local) eval() 23. ├─dplyr::if_else(...) 24. │ └─vctrs::vec_if_else(...) 25. └─rlang::abort(message = message, call = call) Execution halted Package: dm Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'copy_dm_to.Rd': ‘[dplyr:src_dbi]{dplyr::src_dbi}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: doublIn Check: R code for possible problems New result: NOTE Visualize_contact_tracing_data : prepare_network: no visible binding for global variable ‘id’ Visualize_contact_tracing_data : : no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: DrugExposureDiagnostics Check: tests New result: ERROR Running ‘testthat.R’ [361s/356s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(DrugExposureDiagnostics) > > test_check("DrugExposureDiagnostics") Attaching package: 'plotly' The following object is masked from 'package:ggplot2': last_plot The following object is masked from 'package:stats': filter The following object is masked from 'package:graphics': layout Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:09:10.755044 v Summary finished, at 2026-02-01 18:09:11.791377 population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:09:40.383167 v Summary finished, at 2026-02-01 18:09:41.844117 population after earliestStartDate smaller than sample, sampling ignored Saving _problems/test-SummariseChecks-213.R i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:10:03.19248 v Summary finished, at 2026-02-01 18:10:04.084166 i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:10:07.099813 v Summary finished, at 2026-02-01 18:10:08.064642 Progress: getting descendant concepts of ingredient (1125315) used in database Progress: getting descendant concepts of ingredient Progress: adding drug strength info Progress: limiting to concepts in the db Progress: adding concept names Overall time taken: 0 minutes and 1 seconds Time taken: 0 minutes and 1 seconds Progress: getting drug records for ingredient Time taken: 0 minutes and 0 seconds Progress: get concepts used Time taken: 0 minutes and 0 seconds Progress: sampling drug records population after earliestStartDate smaller than sample, sampling ignored Time taken: 0 minutes and 0 seconds Progress: check drugsMissing Time taken: 0 minutes and 2 seconds Progress: check ExposureDuration Time taken: 0 minutes and 0 seconds Progress: check drugQuantity Time taken: 0 minutes and 0 seconds Finished i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:11:04.924139 v Summary finished, at 2026-02-01 18:11:06.448452 population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:12:22.40517 v Summary finished, at 2026-02-01 18:12:23.39404 population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored Saving _problems/test-executeChecks-373.R i The following estimates will be calculated: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-01 18:13:52.306772 v Summary finished, at 2026-02-01 18:13:53.305354 Time taken: 0 minutes and 0 seconds testMessage [ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • Skipping (1): 'test-shiny.R:2:3' • Sys.getenv("TESTDB_USER2222") == "" is TRUE (1): 'test-SyntheaSqlServer.R:5:3' • does not work with latest omopgenerics (3): 'test-runBenchmark.R:2:3', 'test-runBenchmark.R:36:3', 'test-runBenchmark.R:47:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-SummariseChecks.R:213:3'): summariseChecks partial inputs with combination of not empty and empty ingredient: summary of missing and quantity and dose ── Error in `bind_rows(...)`: Can't combine `..1$dose_form` and `..2$dose_form` . Backtrace: ▆ 1. ├─DrugExposureDiagnostics::executeChecks(...) at test-SummariseChecks.R:213:3 2. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList))) 3. │ └─base (local) ``(f = ``, ``, ``) 4. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 5. │ └─base (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) 6. │ └─dplyr (local) rbind(deparse.level, ...) 7. │ └─dplyr::bind_rows(...) 8. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env()) 9. │ └─vctrs (local) ``() 10. │ └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...) 11. │ └─vctrs:::rww_ptype2(x, y, ...) 12. │ ├─dplyr::rowwise(df_ptype2(x, y, ...)) 13. │ └─vctrs::df_ptype2(x, y, ...) 14. └─vctrs (local) ``() 15. └─vctrs::vec_default_ptype2(...) 16. ├─base::withRestarts(...) 17. │ └─base (local) withOneRestart(expr, restarts[[1L]]) 18. │ └─base (local) doWithOneRestart(return(expr), restart) 19. └─vctrs::stop_incompatible_type(...) 20. └─vctrs:::stop_incompatible(...) 21. └─vctrs:::stop_vctrs(...) 22. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) ── Error ('test-executeChecks.R:370:3'): results from multiple ingredients should be joined also if there is one in between that doesn't exist ── Error in `bind_rows(...)`: Can't combine `..1$dose_form` and `..2$dose_form` . Backtrace: ▆ 1. ├─DrugExposureDiagnostics (local) executeChecksMock(...) at test-executeChecks.R:370:3 2. │ └─DrugExposureDiagnostics::executeChecks(...) at test-executeChecks.R:14:3 3. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList))) 4. │ └─base (local) ``(f = ``, ``, ``, ``) 5. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 6. │ └─base (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]) 7. │ └─dplyr (local) rbind(deparse.level, ...) 8. │ └─dplyr::bind_rows(...) 9. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env()) 10. │ └─vctrs (local) ``() 11. │ └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...) 12. │ └─vctrs:::rww_ptype2(x, y, ...) 13. │ ├─dplyr::rowwise(df_ptype2(x, y, ...)) 14. │ └─vctrs::df_ptype2(x, y, ...) 15. └─vctrs (local) ``() 16. └─vctrs::vec_default_ptype2(...) 17. ├─base::withRestarts(...) 18. │ └─base (local) withOneRestart(expr, restarts[[1L]]) 19. │ └─base (local) doWithOneRestart(return(expr), restart) 20. └─vctrs::stop_incompatible_type(...) 21. └─vctrs:::stop_incompatible(...) 22. └─vctrs:::stop_vctrs(...) 23. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) [ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ] Error: ! Test failures. Execution halted Package: dtplyr Check: tests New result: ERROR Running ‘testthat.R’ [17s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(dtplyr) > > test_check("dtplyr") Saving _problems/test-step-group-31.R [ FAIL 1 | WARN 0 | SKIP 35 | PASS 756 ] ══ Skipped tests (35) ══════════════════════════════════════════════════════════ • On CRAN (34): 'test-count.R:15:1', 'test-step-call-pivot_longer.R:47:1', 'test-step-call-pivot_longer.R:88:1', 'test-step-call-pivot_longer.R:142:1', 'test-step-call-pivot_wider.R:95:1', 'test-step-call-pivot_wider.R:131:1', 'test-step-call-pivot_wider.R:143:1', 'test-step-call-pivot_wider.R:156:1', 'test-step-call.R:62:1', 'test-step-call.R:70:1', 'test-step-call.R:136:1', 'test-step-call.R:179:1', 'test-step-colorder-relocate.R:62:1', 'test-step-colorder.R:25:1', 'test-step-colorder.R:41:1', 'test-step-join.R:346:1', 'test-step-mutate.R:148:1', 'test-step-subset-filter.R:111:1', 'test-step-subset-select.R:35:1', 'test-step-subset-select.R:122:1', 'test-step-subset-separate.R:47:1', 'test-step-subset-slice.R:142:1', 'test-step-subset-slice.R:173:1', 'test-step-subset-summarise.R:94:1', 'test-step.R:23:1', 'test-step.R:32:1', 'test-tidyeval-across.R:86:1', 'test-tidyeval-across.R:95:1', 'test-tidyeval-across.R:287:1', 'test-tidyeval-across.R:295:1', 'test-tidyeval.R:183:1', 'test-tidyeval.R:297:1', 'test-tidyeval.R:404:1', 'test-unite.R:69:1' • tidyselect issue #221 (1): 'test-tidyeval-across.R:305:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-step-group.R:29:3'): can add groups if requested ─────────────── Error: The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. i Please use the `.add` argument instead. Backtrace: ▆ 1. ├─dt %>% group_by(x) %>% group_by(y, add = TRUE) 2. ├─dplyr::group_by(., y, add = TRUE) 3. └─dtplyr:::group_by.dtplyr_step(., y, add = TRUE) 4. ├─base::eval(expr(dplyr::group_by_prepare(.data, !!!dots, .add = .add))) 5. │ └─base::eval(expr(dplyr::group_by_prepare(.data, !!!dots, .add = .add))) 6. └─dplyr::group_by_prepare(.data, y = y, add = TRUE, .add = .add) 7. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 35 | PASS 756 ] Error: ! Test failures. Execution halted Package: duckplyr Check: R code for possible problems New result: NOTE summarise.duckplyr_df: no visible global function definition for ‘summarise_deprecate_variable_size’ Undefined global functions or variables: summarise_deprecate_variable_size Package: duckplyr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘developers.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘developers.Rmd’ --- re-building ‘duckdb.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘duckdb.Rmd’ --- re-building ‘extend.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘extend.Rmd’ --- re-building ‘fallback.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘fallback.Rmd’ --- re-building ‘large.Rmd’ using rmarkdown Quitting from large.Rmd:321-325 [unnamed-chunk-23] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `count()`: ! This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. ℹ See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure --- Backtrace: ▆ 1. ├─dplyr::group_by(count(flights_parquet, Month, DayofMonth), Month) 2. ├─dplyr::count(flights_parquet, Month, DayofMonth) 3. ├─duckplyr:::count.duckplyr_df(flights_parquet, Month, DayofMonth) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─rlang::try_fetch(rel, error = identity) 6. │ │ ├─base::tryCatch(...) 7. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. │ │ └─base::withCallingHandlers(...) 11. │ └─dplyr:::tally_n(...) 12. │ └─rlang::quo_is_null(wt) 13. └─rlang::abort(message = message) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'large.Rmd' failed with diagnostics: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. ℹ See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure --- failed re-building ‘large.Rmd’ --- re-building ‘limits.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘limits.Rmd’ --- re-building ‘prudence.Rmd’ using rmarkdown Quitting from prudence.Rmd:288-292 [unnamed-chunk-16] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `count()`: ! This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. ℹ See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure --- Backtrace: ▆ 1. ├─base::nrow(count(flights_partial, origin)) 2. ├─dplyr::count(flights_partial, origin) 3. ├─duckplyr:::count.duckplyr_df(flights_partial, origin) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─rlang::try_fetch(rel, error = identity) 6. │ │ ├─base::tryCatch(...) 7. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. │ │ └─base::withCallingHandlers(...) 11. │ └─dplyr:::tally_n(...) 12. │ └─rlang::quo_is_null(wt) 13. └─rlang::abort(message = message) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'prudence.Rmd' failed with diagnostics: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. ℹ See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure --- failed re-building ‘prudence.Rmd’ --- re-building ‘telemetry.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘telemetry.Rmd’ SUMMARY: processing the following files failed: ‘large.Rmd’ ‘prudence.Rmd’ Error: Vignette re-building failed. Execution halted Package: duckplyr Check: tests New result: ERROR Running ‘testthat.R’ [172s/174s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(duckplyr) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 2. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. > > test_check("duckplyr") Saving _problems/test-tpch-133.R Saving _problems/test-tpch-270.R Saving _problems/test-as_duckplyr_df-268.R Saving _problems/test-as_duckplyr_df-281.R Saving _problems/test-as_duckplyr_df-294.R Saving _problems/test-as_duckplyr_df-307.R Saving _problems/test-as_duckplyr_df-320.R Saving _problems/test-as_duckplyr_df-333.R Saving _problems/test-dplyr-count-tally-190.R Saving _problems/test-dplyr-across-571.R Saving _problems/test-dplyr-across-971.R Saving _problems/test-dplyr-across-1153.R Saving _problems/test-dplyr-generics-153.R Saving _problems/test-dplyr-group-by-103.R Saving _problems/test-dplyr-group-data-63.R Saving _problems/test-dplyr-group-data-86.R Saving _problems/test-dplyr-if-else-119.R Saving _problems/test-dplyr-join-rows-442.R Saving _problems/test-dplyr-select-helpers-20.R Saving _problems/test-dplyr-summarise-23.R Saving _problems/test-dplyr-summarise-152.R Saving _problems/test-dplyr-summarise-571.R Saving _problems/test-prudence-44.R Saving _problems/test-prudence-53.R [ FAIL 24 | WARN 46 | SKIP 592 | PASS 2317 ] ══ Skipped tests (592) ═════════════════════════════════════════════════════════ • Always returns tibble (1): 'test-as_duckplyr_df.R:743:3' • External vector? (4): 'test-as_duckplyr_df.R:2366:3', 'test-as_duckplyr_df.R:2382:3', 'test-as_duckplyr_df.R:2396:3', 'test-as_duckplyr_df.R:2412:3' • Grouped (4): 'test-as_duckplyr_df.R:669:3', 'test-as_duckplyr_df.R:727:3', 'test-as_duckplyr_df.R:789:3', 'test-as_duckplyr_df.R:2658:3' • Hack (1): 'test-as_duckplyr_df.R:560:3' • Missing or empty names not allowed. (6): 'test-dplyr-mutate.R:909:3', 'test-dplyr-filter.R:653:3', 'test-dplyr-select.R:47:3', 'test-dplyr-select.R:143:3', 'test-dplyr-select.R:152:3', 'test-dplyr-summarise.R:469:3' • Must pass a plain data frame or a tibble, not NULL. (1): 'test-dplyr-copy-to.R:19:3' • Must pass a plain data frame or a tibble, not a object. (2): 'test-dplyr-filter.R:584:3', 'test-dplyr-arrange.R:306:3' • Must pass a plain data frame or a tibble, not a object. (1): 'test-dplyr-select.R:183:3' • Must pass a plain data frame or a tibble, not a object. (4): 'test-dplyr-filter.R:573:3', 'test-dplyr-arrange.R:295:3', 'test-dplyr-group-split.R:122:3', 'test-dplyr-group-split.R:137:3' • Must pass a plain data frame or a tibble, not a object. (205): 'test-dplyr-mutate.R:14:3', 'test-dplyr-mutate.R:56:3', 'test-dplyr-mutate.R:84:3', 'test-dplyr-mutate.R:116:3', 'test-dplyr-mutate.R:156:3', 'test-dplyr-mutate.R:176:3', 'test-dplyr-mutate.R:249:3', 'test-dplyr-mutate.R:263:3', 'test-dplyr-mutate.R:300:3', 'test-dplyr-mutate.R:309:3', 'test-dplyr-mutate.R:321:3', 'test-dplyr-mutate.R:407:3', 'test-dplyr-mutate.R:432:3', 'test-dplyr-mutate.R:462:3', 'test-dplyr-mutate.R:492:3', 'test-dplyr-mutate.R:587:3', 'test-dplyr-mutate.R:634:3', 'test-dplyr-mutate.R:643:3', 'test-dplyr-mutate.R:672:3', 'test-dplyr-mutate.R:681:3', 'test-dplyr-mutate.R:702:3', 'test-dplyr-mutate.R:753:3', 'test-dplyr-mutate.R:778:3', 'test-dplyr-mutate.R:799:3', 'test-dplyr-mutate.R:899:3', 'test-dplyr-filter.R:15:5', 'test-dplyr-filter.R:34:3', 'test-dplyr-filter.R:61:3', 'test-dplyr-filter.R:124:3', 'test-dplyr-filter.R:164:3', 'test-dplyr-filter.R:191:3', 'test-dplyr-filter.R:235:3', 'test-dplyr-filter.R:243:3', 'test-dplyr-filter.R:309:3', 'test-dplyr-filter.R:325:3', 'test-dplyr-filter.R:367:3', 'test-dplyr-filter.R:418:3', 'test-dplyr-filter.R:443:3', 'test-dplyr-filter.R:550:3', 'test-dplyr-filter.R:626:3', 'test-dplyr-filter.R:638:3', 'test-dplyr-filter.R:709:3', 'test-dplyr-count-tally.R:64:3', 'test-dplyr-count-tally.R:73:3', 'test-dplyr-count-tally.R:84:3', 'test-dplyr-count-tally.R:166:3', 'test-dplyr-count-tally.R:182:3', 'test-dplyr-across.R:21:3', 'test-dplyr-across.R:28:3', 'test-dplyr-across.R:222:3', 'test-dplyr-across.R:330:3', 'test-dplyr-across.R:340:3', 'test-dplyr-across.R:685:3', 'test-dplyr-across.R:700:5', 'test-dplyr-across.R:1104:3', 'test-dplyr-across.R:1197:3', 'test-dplyr-across.R:1235:3', 'test-dplyr-across.R:1262:3', 'test-dplyr-across.R:1412:3', 'test-dplyr-across.R:1426:3', 'test-dplyr-arrange.R:16:3', 'test-dplyr-arrange.R:213:3', 'test-dplyr-arrange.R:220:3', 'test-dplyr-arrange.R:226:3', 'test-dplyr-arrange.R:344:3', 'test-dplyr-arrange.R:388:3', 'test-dplyr-bind-rows.R:88:3', 'test-dplyr-conditions.R:10:3', 'test-dplyr-context.R:16:3', 'test-dplyr-context.R:30:3', 'test-dplyr-context.R:38:3', 'test-dplyr-context.R:57:3', 'test-dplyr-distinct.R:57:3', 'test-dplyr-distinct.R:63:3', 'test-dplyr-distinct.R:71:3', 'test-dplyr-distinct.R:122:3', 'test-dplyr-distinct.R:163:3', 'test-dplyr-group-by.R:14:3', 'test-dplyr-group-by.R:25:3', 'test-dplyr-group-by.R:54:3', 'test-dplyr-group-by.R:65:3', 'test-dplyr-group-by.R:77:3', 'test-dplyr-group-by.R:86:3', 'test-dplyr-group-by.R:94:3', 'test-dplyr-group-by.R:124:5', 'test-dplyr-group-by.R:132:3', 'test-dplyr-group-by.R:176:3', 'test-dplyr-group-by.R:187:3', 'test-dplyr-group-by.R:202:3', 'test-dplyr-group-by.R:235:3', 'test-dplyr-group-by.R:252:3', 'test-dplyr-group-by.R:283:7', 'test-dplyr-group-by.R:298:3', 'test-dplyr-group-by.R:317:3', 'test-dplyr-group-by.R:325:3', 'test-dplyr-group-by.R:355:3', 'test-dplyr-group-by.R:365:3', 'test-dplyr-group-by.R:375:3', 'test-dplyr-group-by.R:381:3', 'test-dplyr-group-by.R:387:3', 'test-dplyr-group-by.R:424:3', 'test-dplyr-group-by.R:444:3', 'test-dplyr-group-by.R:467:3', 'test-dplyr-group-by.R:485:3', 'test-dplyr-group-by.R:503:3', 'test-dplyr-group-by.R:590:3', 'test-dplyr-group-by.R:614:3', 'test-dplyr-group-data.R:56:3', 'test-dplyr-group-data.R:95:3', 'test-dplyr-group-data.R:103:3', 'test-dplyr-group-data.R:123:3', 'test-dplyr-group-data.R:131:3', 'test-dplyr-group-map.R:9:3', 'test-dplyr-group-map.R:27:3', 'test-dplyr-group-map.R:41:3', 'test-dplyr-group-map.R:66:3', 'test-dplyr-group-map.R:78:3', 'test-dplyr-group-map.R:90:3', 'test-dplyr-group-map.R:111:3', 'test-dplyr-group-map.R:127:3', 'test-dplyr-group-nest.R:35:3', 'test-dplyr-group-nest.R:49:3', 'test-dplyr-group-split.R:40:3', 'test-dplyr-group-split.R:50:3', 'test-dplyr-group-split.R:79:3', 'test-dplyr-group-split.R:104:3', 'test-dplyr-group-trim.R:13:3', 'test-dplyr-group-trim.R:21:3', 'test-dplyr-grouped-df.R:13:3', 'test-dplyr-grouped-df.R:99:3', 'test-dplyr-join.R:630:3', 'test-dplyr-join.R:652:3', 'test-dplyr-join.R:675:3', 'test-dplyr-nest-by.R:26:3', 'test-dplyr-pick.R:40:3', 'test-dplyr-pick.R:77:3', 'test-dplyr-pick.R:100:3', 'test-dplyr-pick.R:141:3', 'test-dplyr-pick.R:166:3', 'test-dplyr-pick.R:199:3', 'test-dplyr-pick.R:223:3', 'test-dplyr-pick.R:271:3', 'test-dplyr-pick.R:377:3', 'test-dplyr-rank.R:58:3', 'test-dplyr-rank.R:104:3', 'test-dplyr-reframe.R:33:3', 'test-dplyr-reframe.R:51:3', 'test-dplyr-reframe.R:85:3', 'test-dplyr-reframe.R:101:3', 'test-dplyr-reframe.R:123:3', 'test-dplyr-reframe.R:136:3', 'test-dplyr-reframe.R:211:3', 'test-dplyr-reframe.R:219:3', 'test-dplyr-reframe.R:231:3', 'test-dplyr-reframe.R:241:3', 'test-dplyr-reframe.R:296:3', 'test-dplyr-rename.R:16:3', 'test-dplyr-rename.R:38:3', 'test-dplyr-rowwise.R:69:3', 'test-dplyr-sample.R:28:3', 'test-dplyr-sample.R:46:3', 'test-dplyr-sample.R:100:3', 'test-dplyr-select-helpers.R:13:3', 'test-dplyr-select.R:11:3', 'test-dplyr-select.R:19:3', 'test-dplyr-select.R:35:3', 'test-dplyr-select.R:94:3', 'test-dplyr-select.R:113:3', 'test-dplyr-sets.R:45:3', 'test-dplyr-slice.R:15:3', 'test-dplyr-slice.R:28:3', 'test-dplyr-slice.R:38:3', 'test-dplyr-slice.R:55:3', 'test-dplyr-slice.R:86:3', 'test-dplyr-slice.R:106:3', 'test-dplyr-slice.R:130:3', 'test-dplyr-slice.R:142:3', 'test-dplyr-slice.R:209:3', 'test-dplyr-slice.R:341:3', 'test-dplyr-slice.R:400:3', 'test-dplyr-slice.R:594:3', 'test-dplyr-slice.R:620:3', 'test-dplyr-slice.R:641:3', 'test-dplyr-summarise.R:52:3', 'test-dplyr-summarise.R:68:3', 'test-dplyr-summarise.R:83:3', 'test-dplyr-summarise.R:126:3', 'test-dplyr-summarise.R:200:3', 'test-dplyr-summarise.R:219:3', 'test-dplyr-summarise.R:236:3', 'test-dplyr-summarise.R:241:3', 'test-dplyr-summarise.R:251:3', 'test-dplyr-summarise.R:265:3', 'test-dplyr-summarise.R:271:3', 'test-dplyr-summarise.R:302:3', 'test-dplyr-summarise.R:314:3', 'test-dplyr-summarise.R:354:3', 'test-dplyr-summarise.R:367:3', 'test-dplyr-summarise.R:375:3', 'test-dplyr-summarise.R:435:3', 'test-dplyr-transmute.R:9:3', 'test-dplyr-transmute.R:16:3', 'test-dplyr-transmute.R:34:3', 'test-dplyr-transmute.R:56:3', 'test-dplyr-transmute.R:89:3' • Must pass a plain data frame or a tibble, not a object. (1): 'test-dplyr-summarise.R:92:3' • Must pass a plain data frame or a tibble, not a object. (1): 'test-dplyr-slice.R:386:3' • Must pass a plain data frame or a tibble, not a object. (34): 'test-dplyr-mutate.R:336:3', 'test-dplyr-mutate.R:367:3', 'test-dplyr-mutate.R:373:3', 'test-dplyr-mutate.R:380:3', 'test-dplyr-mutate.R:414:3', 'test-dplyr-mutate.R:472:3', 'test-dplyr-mutate.R:596:3', 'test-dplyr-mutate.R:742:3', 'test-dplyr-mutate.R:767:3', 'test-dplyr-mutate.R:784:3', 'test-dplyr-filter.R:229:3', 'test-dplyr-filter.R:718:3', 'test-dplyr-across.R:1163:3', 'test-dplyr-across.R:1289:3', 'test-dplyr-group-by.R:267:3', 'test-dplyr-group-data.R:117:3', 'test-dplyr-group-split.R:44:3', 'test-dplyr-group-split.R:111:3', 'test-dplyr-join.R:499:3', 'test-dplyr-join.R:685:3', 'test-dplyr-nest-by.R:13:3', 'test-dplyr-pick.R:65:3', 'test-dplyr-pick.R:88:3', 'test-dplyr-pick.R:332:3', 'test-dplyr-reframe.R:249:3', 'test-dplyr-reframe.R:259:3', 'test-dplyr-reframe.R:268:3', 'test-dplyr-reframe.R:305:3', 'test-dplyr-rowwise.R:11:3', 'test-dplyr-rowwise.R:46:3', 'test-dplyr-rowwise.R:78:3', 'test-dplyr-slice.R:218:3', 'test-dplyr-summarise.R:285:3', 'test-dplyr-summarise.R:444:3' • Must pass a plain data frame or a tibble, not a character vector. (1): 'test-dplyr-group-nest.R:19:3' • Must pass a plain data frame or a tibble, not a number. (1): 'test-dplyr-sets.R:143:3' • Must pass a plain data frame or a tibble, not an integer vector. (1): 'test-dplyr-sets.R:53:3' • On CRAN (269): 'test-dplyr-mutate.R:200:1', 'test-dplyr-filter.R:424:1', 'test-dplyr-filter.R:433:1', 'test-dplyr-filter.R:697:1', 'test-dplyr-filter.R:723:1', 'test-dplyr-count-tally.R:51:1', 'test-dplyr-count-tally.R:141:1', 'test-dplyr-count-tally.R:169:1', 'test-dplyr-count-tally.R:193:1', 'test-dplyr-count-tally.R:225:1', 'test-as_duckplyr_tibble.R:1:1', 'test-as_duckplyr_tibble.R:15:1', 'test-compute.R:1:1', 'test-demo.R:1:1', 'test-dplyr-across.R:143:1', 'test-dplyr-across.R:156:1', 'test-dplyr-across.R:227:1', 'test-dplyr-across.R:621:1', 'test-dplyr-across.R:758:1', 'test-dplyr-across.R:795:1', 'test-dplyr-across.R:1183:1', 'test-dplyr-across.R:1321:1', 'test-dplyr-across.R:1333:1', 'test-dplyr-all-equal.R:8:1', 'test-dplyr-all-equal.R:32:1', 'test-dplyr-all-equal.R:41:1', 'test-dplyr-all-equal.R:50:1', 'test-dplyr-all-equal.R:60:1', 'test-dplyr-all-equal.R:114:1', 'test-dplyr-all-equal.R:143:1', 'test-dplyr-all-equal.R:155:1', 'test-dplyr-all-equal.R:167:1', 'test-dplyr-all-equal.R:175:1', 'test-dplyr-arrange.R:34:1', 'test-dplyr-arrange.R:175:1', 'test-dplyr-arrange.R:181:1', 'test-dplyr-arrange.R:193:1', 'test-dplyr-arrange.R:326:1', 'test-dplyr-bind-cols.R:46:1', 'test-dplyr-bind-cols.R:122:1', 'test-dplyr-bind-cols.R:138:1', 'test-dplyr-bind-rows.R:140:1', 'test-dplyr-bind-rows.R:155:1', 'test-dplyr-bind-rows.R:248:1', 'test-dplyr-by.R:74:1', 'test-dplyr-by.R:82:1', 'test-dplyr-by.R:91:1', 'test-dplyr-by.R:100:1', 'test-dplyr-case-match.R:29:1', 'test-dplyr-case-match.R:44:1', 'test-dplyr-case-match.R:56:1', 'test-dplyr-case-match.R:65:1', 'test-dplyr-case-when.R:222:1', 'test-dplyr-case-when.R:231:1', 'test-dplyr-case-when.R:243:1', 'test-dplyr-case-when.R:253:1', 'test-dplyr-case-when.R:259:1', 'test-dplyr-case-when.R:268:1', 'test-dplyr-case-when.R:277:1', 'test-dplyr-coalesce.R:32:1', 'test-dplyr-coalesce.R:94:1', 'test-dplyr-coalesce.R:102:1', 'test-dplyr-coalesce.R:118:1', 'test-dplyr-coalesce.R:124:1', 'test-dplyr-conditions.R:45:1', 'test-dplyr-consecutive-id.R:17:1', 'test-dplyr-consecutive-id.R:26:1', 'test-dplyr-context.R:63:1', 'test-dplyr-desc.R:8:1', 'test-dplyr-distinct.R:185:1', 'test-dplyr-funs.R:60:1', 'test-dplyr-funs.R:75:1', 'test-dplyr-grouped-df.R:123:1', 'test-dplyr-grouped-df.R:193:1', 'test-dplyr-if-else.R:53:1', 'test-dplyr-if-else.R:61:1', 'test-dplyr-if-else.R:78:1', 'test-dplyr-if-else.R:84:1', 'test-dplyr-if-else.R:99:1', 'test-dplyr-if-else.R:105:1', 'test-dplyr-join-by.R:195:1', 'test-dplyr-join-by.R:239:1', 'test-dplyr-join-by.R:246:1', 'test-dplyr-join-by.R:263:1', 'test-dplyr-join-by.R:271:1', 'test-dplyr-join-by.R:358:1', 'test-dplyr-join-by.R:373:1', 'test-dplyr-join-cols.R:90:1', 'test-dplyr-join-cols.R:131:1', 'test-dplyr-join-cols.R:136:1', 'test-dplyr-join-cols.R:196:1', 'test-dplyr-join-cross.R:57:1', 'test-dplyr-join-rows.R:8:1', 'test-dplyr-join-rows.R:155:1', 'test-dplyr-join-rows.R:170:1', 'test-dplyr-join-rows.R:178:1', 'test-dplyr-join-rows.R:187:1', 'test-dplyr-join-rows.R:193:1', 'test-dplyr-join-rows.R:212:1', 'test-dplyr-join-rows.R:276:1', 'test-dplyr-join-rows.R:386:1', 'test-dplyr-join-rows.R:405:1', 'test-dplyr-join-rows.R:422:3', 'test-dplyr-join-rows.R:451:1', 'test-dplyr-join-rows.R:463:1', 'test-dplyr-join.R:152:1', 'test-dplyr-join.R:340:1', 'test-dplyr-join.R:352:1', 'test-dplyr-join.R:387:1', 'test-dplyr-join.R:393:1', 'test-dplyr-join.R:449:1', 'test-dplyr-join.R:458:1', 'test-dplyr-join.R:467:1', 'test-dplyr-join.R:516:1', 'test-dplyr-join.R:552:1', 'test-dplyr-join.R:602:1', 'test-dplyr-join.R:704:1', 'test-dplyr-join.R:716:1', 'test-dplyr-join.R:727:1', 'test-dplyr-join.R:748:1', 'test-dplyr-join.R:765:1', 'test-dplyr-lead-lag.R:26:1', 'test-dplyr-lead-lag.R:59:1', 'test-dplyr-lead-lag.R:70:1', 'test-dplyr-lead-lag.R:79:1', 'test-dplyr-n-distinct.R:46:1', 'test-dplyr-na-if.R:67:1', 'test-dplyr-na-if.R:75:1', 'test-dplyr-na-if.R:87:1', 'test-dplyr-nth-value.R:145:1', 'test-dplyr-nth-value.R:154:1', 'test-dplyr-nth-value.R:160:1', 'test-dplyr-nth-value.R:166:1', 'test-dplyr-nth-value.R:178:1', 'test-dplyr-nth-value.R:184:1', 'test-dplyr-order-by.R:8:1', 'test-dplyr-order-by.R:22:1', 'test-dplyr-order-by.R:50:1', 'test-dplyr-pick.R:148:1', 'test-dplyr-pick.R:306:1', 'test-dplyr-pick.R:336:1', 'test-dplyr-pick.R:346:1', 'test-dplyr-pick.R:462:1', 'test-dplyr-pick.R:486:1', 'test-dplyr-pick.R:497:1', 'test-dplyr-rank.R:107:1', 'test-dplyr-relocate.R:34:1', 'test-dplyr-rename.R:77:1', 'test-dplyr-rename.R:87:1', 'test-dplyr-rename.R:97:1', 'test-dplyr-rows.R:20:1', 'test-dplyr-rows.R:71:1', 'test-dplyr-rows.R:80:1', 'test-dplyr-rows.R:89:1', 'test-dplyr-rows.R:101:1', 'test-dplyr-rows.R:125:1', 'test-dplyr-rows.R:141:1', 'test-dplyr-rows.R:176:1', 'test-dplyr-rows.R:203:1', 'test-dplyr-rows.R:218:1', 'test-dplyr-rows.R:233:1', 'test-dplyr-rows.R:245:1', 'test-dplyr-rows.R:273:1', 'test-dplyr-rows.R:300:1', 'test-dplyr-rows.R:315:1', 'test-dplyr-rows.R:330:1', 'test-dplyr-rows.R:360:1', 'test-dplyr-rows.R:375:1', 'test-dplyr-rows.R:390:1', 'test-dplyr-rows.R:399:1', 'test-dplyr-rows.R:419:1', 'test-dplyr-rows.R:436:1', 'test-dplyr-rows.R:473:1', 'test-dplyr-rows.R:490:1', 'test-dplyr-rows.R:497:1', 'test-dplyr-rows.R:503:1', 'test-dplyr-rows.R:513:1', 'test-dplyr-rows.R:523:1', 'test-dplyr-rows.R:532:1', 'test-dplyr-rowwise.R:62:1', 'test-dplyr-rowwise.R:94:1', 'test-dplyr-sample.R:109:1', 'test-dplyr-select.R:164:1', 'test-dplyr-sets.R:62:1', 'test-dplyr-sets.R:75:1', 'test-dplyr-sets.R:89:1', 'test-dplyr-sets.R:129:1', 'test-dplyr-sets.R:146:1', 'test-dplyr-slice.R:45:1', 'test-dplyr-slice.R:66:1', 'test-dplyr-slice.R:76:1', 'test-dplyr-slice.R:112:1', 'test-dplyr-slice.R:197:1', 'test-dplyr-slice.R:223:1', 'test-dplyr-slice.R:233:1', 'test-dplyr-slice.R:246:1', 'test-dplyr-slice.R:254:1', 'test-dplyr-slice.R:303:1', 'test-dplyr-slice.R:344:1', 'test-dplyr-slice.R:409:1', 'test-dplyr-slice.R:522:1', 'test-dplyr-slice.R:530:1', 'test-dplyr-slice.R:563:1', 'test-dplyr-slice.R:576:1', 'test-dplyr-summarise.R:423:1', 'test-dplyr-transmute.R:96:1', 'test-duckplyr-across.R:1:1', 'test-duckplyr.R:10:1', 'test-ducktbl.R:30:1', 'test-ducktbl.R:36:1', 'test-ducktbl.R:42:1', 'test-expr.R:2:3', 'test-fallback.R:1:1', 'test-fallback.R:17:1', 'test-fallback.R:33:1', 'test-fallback.R:49:1', 'test-fallback.R:62:1', 'test-fallback.R:81:1', 'test-fallback.R:109:1', 'test-fallback.R:126:1', 'test-fallback.R:143:1', 'test-fallback.R:160:1', 'test-fallback.R:174:1', 'test-fallback.R:186:1', 'test-fallback.R:198:1', 'test-fallback.R:210:1', 'test-fallback.R:226:1', 'test-fallback.R:242:1', 'test-fallback.R:290:1', 'test-handle_desc.R:19:1', 'test-handle_desc.R:28:1', 'test-n_distinct.R:111:1', 'test-n_distinct.R:125:1', 'test-n_distinct.R:138:1', 'test-overwrite.R:1:1', 'test-relational-duckdb.R:1:1', 'test-relational-duckdb.R:60:1', 'test-relational-duckdb.R:66:1', 'test-relational-duckdb.R:103:1', 'test-relational-rel.R:1:1', 'test-relational.R:1:1', 'test-telemetry.R:3:1', 'test-telemetry.R:40:1', 'test-telemetry.R:52:1', 'test-telemetry.R:64:1', 'test-telemetry.R:76:1', 'test-telemetry.R:93:1', 'test-telemetry.R:114:1', 'test-telemetry.R:136:1', 'test-telemetry.R:143:1', 'test-telemetry.R:165:1', 'test-telemetry.R:177:1', 'test-telemetry.R:194:1', 'test-telemetry.R:201:1', 'test-telemetry.R:223:1', 'test-telemetry.R:230:1', 'test-telemetry.R:247:1', 'test-telemetry.R:254:1', 'test-telemetry.R:271:1', 'test-telemetry.R:278:1', 'test-telemetry.R:285:1', 'test-telemetry.R:292:1', 'test-translate.R:9:1', 'test-translate.R:15:1', 'test-translate.R:21:1', 'test-translate.R:40:1', 'test-translate.R:132:1', 'test-translate.R:162:1', 'test-translate.R:199:1' • Random seed (2): 'test-as_duckplyr_df.R:2136:3', 'test-as_duckplyr_df.R:2152:3' • Special (5): 'test-as_duckplyr_df.R:683:3', 'test-as_duckplyr_df.R:699:3', 'test-as_duckplyr_df.R:759:3', 'test-as_duckplyr_df.R:834:3', 'test-as_duckplyr_df.R:1653:3' • Stack overflow (1): 'test-as_duckplyr_df.R:2120:3' • TODO duckdb (17): 'test-dplyr-mutate.R:438:3', 'test-dplyr-mutate.R:558:3', 'test-dplyr-across.R:911:3', 'test-dplyr-across.R:937:3', 'test-dplyr-all-equal.R:187:3', 'test-dplyr-copy-to.R:9:3', 'test-dplyr-funs.R:85:3', 'test-dplyr-funs.R:103:3', 'test-dplyr-generics.R:167:3', 'test-dplyr-group-by.R:570:3', 'test-dplyr-group-nest.R:53:3', 'test-dplyr-join-rows.R:200:3', 'test-dplyr-join.R:363:3', 'test-dplyr-join.R:369:3', 'test-dplyr-summarise.R:37:3', 'test-dplyr-summarise.R:337:3', 'test-dplyr-summarise.R:478:3' • WAT (3): 'test-as_duckplyr_df.R:713:3', 'test-as_duckplyr_df.R:773:3', 'test-as_duckplyr_df.R:1667:3' • Won't need (1): 'test-prom.R:2:3' • argument ".data" is missing, with no default (1): 'test-dplyr-group-data.R:71:3' • dplyr:::compute_groups() is only needed to test dplyr internals (4): 'test-dplyr-group-by.R:579:3', 'test-dplyr-grouped-df.R:202:3', 'test-dplyr-grouped-df.R:208:3', 'test-dplyr-grouped-df.R:219:3' • dplyr:::err_locs() is only needed to test dplyr internals (1): 'test-dplyr-conditions.R:34:3' • dplyr:::expand_pick() is only needed to test dplyr internals (2): 'test-dplyr-pick.R:552:3', 'test-dplyr-pick.R:569:3' • dplyr:::group_labels_details() is only needed to test dplyr internals (1): 'test-dplyr-context.R:76:3' • dplyr:::reset_dplyr_warnings() is only needed to test dplyr internals (4): 'test-dplyr-conditions.R:68:3', 'test-dplyr-conditions.R:135:3', 'test-dplyr-conditions.R:164:3', 'test-dplyr-conditions.R:188:3' • dplyr:::shift() is only needed to test dplyr internals (9): 'test-dplyr-lead-lag.R:94:3', 'test-dplyr-lead-lag.R:104:3', 'test-dplyr-lead-lag.R:113:3', 'test-dplyr-lead-lag.R:125:3', 'test-dplyr-lead-lag.R:140:3', 'test-dplyr-lead-lag.R:151:3', 'test-dplyr-lead-lag.R:159:3', 'test-dplyr-lead-lag.R:168:3', 'test-dplyr-lead-lag.R:174:3' • i In argument: `.result = (1 + "") * am`. (1): 'test-dplyr-conditions.R:25:5' • i In argument: `n = base::sum(...)`. (1): 'test-dplyr-count-tally.R:127:3' • {RSQLite} is not installed (2): 'test-dplyr-count-tally.R:93:3', 'test-dplyr-count-tally.R:105:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-tpch.R:110:3'): TPCH queries can be parsed and run ───────────── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─duckplyr:::tpch_21() 2. │ └─... %>% filter(n_supplier > 1) 3. ├─dplyr::filter(., n_supplier > 1) 4. ├─dplyr::summarise(., n_supplier = n(), .by = l_orderkey) 5. ├─dplyr::count(., l_orderkey, l_suppkey) 6. ├─duckplyr:::count.duckplyr_df(., l_orderkey, l_suppkey) 7. │ ├─duckplyr:::rel_try(...) 8. │ │ └─base::force(rel) 9. │ └─dplyr:::tally_n(...) 10. │ └─rlang::quo_is_null(wt) 11. └─rlang::abort(message = message) ── Failure ('test-tpch.R:247:3'): TPCH queries can be parsed and run with overwriting ── Expected `{ ... }` not to throw any errors. Actually got a with message: `quo` must be a quosure Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-tpch.R:247:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─duckplyr:::tpch_21() at test-tpch.R:268:5 8. │ └─... %>% filter(n_supplier > 1) 9. ├─dplyr::filter(., n_supplier > 1) 10. ├─dplyr::summarise(., n_supplier = n(), .by = l_orderkey) 11. ├─dplyr::count(., l_orderkey, l_suppkey) 12. ├─duckplyr (local) count.data.frame(., l_orderkey, l_suppkey) 13. │ ├─duckplyr:::rel_try(...) 14. │ │ └─base::force(rel) 15. │ └─dplyr:::tally_n(...) 16. │ └─rlang::quo_is_null(wt) 17. └─rlang::abort(message = message) ── Error ('test-as_duckplyr_df.R:268:3'): as_duckplyr_df_impl() and count() ──── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─test_df %>% as_duckplyr_df_impl() %>% count() at test-as_duckplyr_df.R:268:3 2. ├─dplyr::count(.) 3. ├─duckplyr:::count.duckplyr_df(.) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─base::force(rel) 6. │ └─dplyr:::tally_n(...) 7. │ └─rlang::quo_is_null(wt) 8. └─rlang::abort(message = message) ── Error ('test-as_duckplyr_df.R:281:3'): as_duckplyr_df_impl() and count(a) ─── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─test_df %>% as_duckplyr_df_impl() %>% count(a) at test-as_duckplyr_df.R:281:3 2. ├─dplyr::count(., a) 3. ├─duckplyr:::count.duckplyr_df(., a) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─base::force(rel) 6. │ └─dplyr:::tally_n(...) 7. │ └─rlang::quo_is_null(wt) 8. └─rlang::abort(message = message) ── Error ('test-as_duckplyr_df.R:294:3'): as_duckplyr_df_impl() and count(b) ─── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─test_df %>% as_duckplyr_df_impl() %>% count(b) at test-as_duckplyr_df.R:294:3 2. ├─dplyr::count(., b) 3. ├─duckplyr:::count.duckplyr_df(., b) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─base::force(rel) 6. │ └─dplyr:::tally_n(...) 7. │ └─rlang::quo_is_null(wt) 8. └─rlang::abort(message = message) ── Error ('test-as_duckplyr_df.R:307:3'): as_duckplyr_df_impl() and count(g) ─── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─test_df %>% as_duckplyr_df_impl() %>% count(g) at test-as_duckplyr_df.R:307:3 2. ├─dplyr::count(., g) 3. ├─duckplyr:::count.duckplyr_df(., g) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─base::force(rel) 6. │ └─dplyr:::tally_n(...) 7. │ └─rlang::quo_is_null(wt) 8. └─rlang::abort(message = message) ── Error ('test-as_duckplyr_df.R:320:3'): as_duckplyr_df_impl() and count(g, a) ── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─test_df %>% as_duckplyr_df_impl() %>% count(g, a) at test-as_duckplyr_df.R:320:3 2. ├─dplyr::count(., g, a) 3. ├─duckplyr:::count.duckplyr_df(., g, a) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─base::force(rel) 6. │ └─dplyr:::tally_n(...) 7. │ └─rlang::quo_is_null(wt) 8. └─rlang::abort(message = message) ── Error ('test-as_duckplyr_df.R:333:3'): as_duckplyr_df_impl() and count(b, g) ── Error in `quo_is_null(wt)`: `quo` must be a quosure Backtrace: ▆ 1. ├─test_df %>% as_duckplyr_df_impl() %>% count(b, g) at test-as_duckplyr_df.R:333:3 2. ├─dplyr::count(., b, g) 3. ├─duckplyr:::count.duckplyr_df(., b, g) 4. │ ├─duckplyr:::rel_try(...) 5. │ │ └─base::force(rel) 6. │ └─dplyr:::tally_n(...) 7. │ └─rlang::quo_is_null(wt) 8. └─rlang::abort(message = message) ── Error ('test-dplyr-count-tally.R:190:3'): .drop is deprecated ─────────────── Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and is now defunct. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-dplyr-count-tally.R:190:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─duckplyr:::duckplyr_add_count(df, f, .drop = FALSE) 8. ├─dplyr::add_count(x, ...) 9. └─duckplyr:::add_count.duckplyr_df(x, ...) 10. └─dplyr::add_count(...) 11. └─dplyr:::add_count_impl(...) 12. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call) 13. └─lifecycle:::deprecate_stop0(msg) 14. └─rlang::cnd_signal(...) ── Error ('test-dplyr-across.R:571:3'): if_any() and if_all() do not enforce logical ── Error in `filter(.data, ..., .by = { { .by } }, .preserve = .preserve)`: i In argument: `if_all(x:y, identity)`. Caused by error in `if_all()`: ! `x` must be a logical vector, not the number 10. ── Failure ('test-dplyr-across.R:968:3'): if_any() and if_all() wrapped deal with no inputs or single inputs ── Expected `duckplyr_filter(d, (if_any(starts_with("c"), ~FALSE)))` to equal `duckplyr_filter(d)`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 `actual$x`: `expected$x`: 1 ── Failure ('test-dplyr-across.R:1150:3'): expand_if_across() expands lambdas ── Expected `map(expand_if_across(quo), quo_squash)` to equal `alist(cyl > 4 | am > 4)`. Differences: `actual` is length 2 `expected` is length 1 `actual[[1]]` is a symbol `expected[[1]]` is a call `actual[[2]]` is a call `expected[[2]]` is absent ── Failure ('test-dplyr-generics.R:150:3'): `dplyr_reconstruct()` retains attribute ordering of `template` ── Expected `attributes(dplyr_reconstruct(df, df))` to be identical to `attributes(df)`. Differences: `names(actual)`: "names" "row.names" "class" `names(expected)`: "names" "class" "row.names" ── Error ('test-dplyr-group-by.R:103:3'): .dots is soft deprecated ───────────── Error: The `.dots` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-dplyr-group-by.R:103:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─duckplyr:::duckplyr_group_by(df, .dots = "x") 8. ├─dplyr::group_by(.data, ...) 9. └─duckplyr:::group_by.duckplyr_df(.data, ...) 10. └─dplyr::group_by(.data, ..., .add = .add, .drop = .drop) 11. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 12. └─lifecycle::deprecate_stop("1.0.0", "group_by(.dots = )") 13. └─lifecycle:::deprecate_stop0(msg) 14. └─rlang::cnd_signal(...) ── Error ('test-dplyr-group-data.R:63:3'): duckplyr_group_keys(...) is deprecated ── Error: The `...` argument of `group_keys()` was deprecated in dplyr 1.0.0 and is now defunct. i Please `group_by()` first Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-dplyr-group-data.R:63:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─df %>% duckplyr_group_keys(x) 8. └─duckplyr:::duckplyr_group_keys(., x) 9. ├─dplyr::group_keys(.tbl, ...) 10. └─duckplyr:::group_keys.duckplyr_df(.tbl, ...) 11. └─dplyr::group_keys(.tbl, ...) 12. └─lifecycle::deprecate_stop("1.0.0", "group_keys(... = )", details = "Please `group_by()` first") 13. └─lifecycle:::deprecate_stop0(msg) 14. └─rlang::cnd_signal(...) ── Error ('test-dplyr-group-data.R:86:3'): duckplyr_group_indices(...) still works though ── Error: The `...` argument of `group_indices()` was deprecated in dplyr 1.0.0 and is now defunct. i Please `group_by()` first Backtrace: ▆ 1. ├─df %>% duckplyr_group_indices(x) at test-dplyr-group-data.R:86:3 2. └─duckplyr:::duckplyr_group_indices(., x) 3. ├─dplyr::group_indices(.data, ...) 4. └─duckplyr:::group_indices.duckplyr_df(.data, ...) 5. └─dplyr::group_indices(.data, ...) 6. └─lifecycle::deprecate_stop("1.0.0", "group_indices(... = )", details = "Please `group_by()` first") 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) ── Failure ('test-dplyr-if-else.R:117:3'): `size` overrides the `condition` size ── Expected `{ ... }` to throw a error. Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-dplyr-if-else.R:117:3 2. └─testthat:::expect_snapshot_(...) ── Error ('test-dplyr-join-rows.R:440:3'): `multiple = NULL` is deprecated and results in `'all'` (#6731) ── Error in `vctrs::vec_locate_matches(needles = needles, haystack = haystack, condition = condition, filter = filter, incomplete = incomplete, no_match = no_match, remaining = remaining, multiple = multiple, relationship = relationship, needles_arg = needles_arg, haystack_arg = haystack_arg, nan_distinct = TRUE)`: `multiple` must be a string. Backtrace: ▆ 1. ├─dplyr:::join_rows(df1, df2, multiple = NULL) 2. │ └─dplyr:::dplyr_locate_matches(...) 3. │ ├─base::withCallingHandlers(...) 4. │ └─vctrs::vec_locate_matches(...) 5. └─rlang::abort(message = message, call = call) ── Error ('test-dplyr-select-helpers.R:20:3'): group_cols(vars) is deprecated ── Error: The `vars` argument of `group_cols()` was deprecated in dplyr 1.0.0 and is now defunct. i Use `data` with entire dataframe instead Backtrace: ▆ 1. ├─testthat::expect_warning(out <- group_cols("a"), "deprecated") at test-dplyr-select-helpers.R:20:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─dplyr::group_cols("a") 8. └─dplyr:::group_cols_legacy(vars) 9. └─lifecycle::deprecate_stop("1.0.0", "group_cols(vars = )", details = "Use `data` with entire dataframe instead") 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) ── Error ('test-dplyr-summarise.R:20:3'): inputs are recycled (deprecated in 1.1.0) ── Error in `summarise(.data, ..., .by = { { .by } }, .groups = .groups)`: i In argument: `y = 1:3`. Caused by error: ! `y` must be size 1, not 3. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-dplyr-summarise.R:20:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─tibble() %>% duckplyr_summarise(x = 1, y = 1:3, z = 1) 5. ├─duckplyr:::duckplyr_summarise(., x = 1, y = 1:3, z = 1) 6. │ ├─dplyr::summarise(.data, ...) 7. │ └─duckplyr:::summarise.duckplyr_df(.data, ...) 8. │ └─dplyr::summarise(...) 9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 10. │ └─base::withCallingHandlers(...) 11. ├─dplyr:::dplyr_internal_error(...) 12. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 13. │ └─rlang:::signal_abort(cnd, .file) 14. │ └─base::signalCondition(cnd) 15. └─dplyr (local) ``(``) 16. └─dplyr (local) handler(cnd) 17. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-dplyr-summarise.R:152:3'): named data frame results with 0 columns participate in recycling (#6509) ── Error in `summarise(.data, ..., .by = { { .by } }, .groups = .groups)`: i In argument: `empty = empty`. Caused by error: ! `empty` must be size 1, not 0. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-dplyr-summarise.R:152:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─duckplyr:::duckplyr_summarise(df, empty = empty) 5. │ ├─dplyr::summarise(.data, ...) 6. │ └─duckplyr:::summarise.duckplyr_df(.data, ...) 7. │ └─dplyr::summarise(...) 8. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 9. │ └─base::withCallingHandlers(...) 10. ├─dplyr:::dplyr_internal_error(...) 11. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 12. │ └─rlang:::signal_abort(cnd, .file) 13. │ └─base::signalCondition(cnd) 14. └─dplyr (local) ``(``) 15. └─dplyr (local) handler(cnd) 16. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-dplyr-summarise.R:569:3'): non-summary results are deprecated in favor of `duckplyr_reframe()` (#6382) ── Error in `summarise(.data, ..., .by = { { .by } }, .groups = .groups)`: i In argument: `x = which(x < 3)`. Caused by error: ! `x` must be size 1, not 2. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─duckplyr:::duckplyr_summarise(df, x = which(x < 3)) 2. │ ├─dplyr::summarise(.data, ...) 3. │ └─duckplyr:::summarise.duckplyr_df(.data, ...) 4. │ └─dplyr::summarise(...) 5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 6. │ └─base::withCallingHandlers(...) 7. ├─dplyr:::dplyr_internal_error(...) 8. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 9. │ └─rlang:::signal_abort(cnd, .file) 10. │ └─base::signalCondition(cnd) 11. └─dplyr (local) ``(``) 12. └─dplyr (local) handler(cnd) 13. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-prudence.R:43:3'): prudence after operation with failure ─────── Error in `count(., x)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-prudence.R:52:3'): prudence after operation with success ─────── Error in `count(.)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure [ FAIL 24 | WARN 46 | SKIP 592 | PASS 2317 ] Error: ! Test failures. 🛠: 2235 🔨: 1205 🦆: 1030 add_count, anti_join, arrange, arrange.data.frame, compute, count, count.data.frame, cross_join, distinct, distinct.data.frame, do, eval, filter, filter.data.frame, full_join, group_by, group_indices, group_keys, group_map, group_modify, group_nest, group_size, group_split, group_trim, head, inner_join, inner_join.data.frame, intersect, left_join, left_join.data.frame, mutate, mutate.data.frame, n_groups, nest_by, nest_join, pull, reframe, relocate, rename, rename_with, right_join, rows_append, rows_delete, rows_insert, rows_patch, rows_update, rows_upsert, rowwise, select, select.data.frame, semi_join, semi_join.data.frame, setdiff, setequal, slice, slice_head, slice_head.data.frame, slice_sample, slice_tail, summarise, summarise.data.frame, symdiff, transmute, ungroup, union_all 00:02:50.873628 Execution halted Package: dyngen Check: examples New result: ERROR Running examples in ‘dyngen-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_timings > ### Title: Return the timings of each of the dyngen steps > ### Aliases: get_timings > > ### ** Examples > > data("example_model") > timings <- get_timings(example_model) Error in `summarise()`: ℹ In argument: `task = .data$task[-length(.data$task)]`. ℹ In group 2: `group = "2_tf_network"`. Caused by error: ! `task` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─dyngen::get_timings(example_model) 2. │ └─model$timings %>% group_by(.data$group) %>% ... 3. ├─dplyr::summarise(...) 4. ├─dplyr:::summarise.grouped_df(...) 5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 6. │ └─base::withCallingHandlers(...) 7. ├─dplyr:::dplyr_internal_error(...) 8. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 9. │ └─rlang:::signal_abort(cnd, .file) 10. │ └─base::signalCondition(cnd) 11. └─dplyr (local) ``(``) 12. └─dplyr (local) handler(cnd) 13. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: dynwrap Check: R code for possible problems New result: NOTE get_ti_methods: no visible binding for global variable ‘id’ simplify_replace_edges: no visible binding for global variable ‘id’ simplify_trajectory: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: edeaR Check: R code for possible problems New result: NOTE plot_trace_coverage: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: ediblecity Check: R code for possible problems New result: NOTE UHI: no visible binding for global variable ‘location’ green_capita: no visible binding for global variable ‘location’ no2_seq: no visible binding for global variable ‘location’ runoff_prev: no visible binding for global variable ‘id’ Undefined global functions or variables: id location Package: EEAaq Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignettes.Rmd’ using rmarkdown Quitting from vignettes.Rmd:108-110 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarise()`: ℹ In argument: `gap = lubridate::interval(.data$DatetimeBegin, .data$DatetimeBegin[-1])`. ℹ In group 1: `AirQualityStationEoICode = "IT0477A"`. Caused by error: ! `gap` must be size 1, not 1100. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─EEAaq::EEAaq_summary(data = data) 2. │ └─base::lapply(pollutant, g_length, data = data) 3. │ └─EEAaq (local) FUN(X[[i]], ...) 4. │ └─... %>% dplyr::tibble() 5. ├─dplyr::tibble(.) 6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair) 7. │ └─rlang::eval_tidy(xs[[j]], mask) 8. ├─base::suppressWarnings(.) 9. │ └─base::withCallingHandlers(...) 10. ├─dplyr::mutate(...) 11. ├─base::as.data.frame(.) 12. ├─dplyr::summarise(...) 13. ├─dplyr::filter(., .data$gap > 0) 14. ├─dplyr::mutate(., gap = lubridate::time_length(.data$gap, unit = "hour")) 15. ├─dplyr::summarise(...) 16. ├─dplyr:::summarise.grouped_df(...) 17. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 18. │ └─base::withCallingHandlers(...) 19. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'vignettes.Rmd' failed with diagnostics: ℹ In argument: `gap = lubridate::interval(.data$DatetimeBegin, .data$DatetimeBegin[-1])`. ℹ In group 1: `AirQualityStationEoICode = "IT0477A"`. Caused by error: ! `gap` must be size 1, not 1100. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘vignettes.Rmd’ SUMMARY: processing the following file failed: ‘vignettes.Rmd’ Error: Vignette re-building failed. Execution halted Package: eesim Check: examples New result: ERROR Running examples in ‘eesim-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: calendar_plot > ### Title: Create calendar plot > ### Aliases: calendar_plot > > ### ** Examples > > testdat <- sim_exposure(n = 1000, central = 0.1, + exposure_type = "binary") > testdat$x[c(89,101,367,500,502,598,678,700,895)] <- 3 > calendar_plot(testdat, type = "discrete", labels = c("no", "yes", "maybe")) Error: ! `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─eesim::calendar_plot(...) 2. │ └─... %>% ... 3. ├─ggplot2::ggplot(., ggplot2::aes_(x = ~Weekday, y = ~Week, fill = ~Exposure)) 4. ├─dplyr::ungroup(.) 5. └─dplyr::mutate_(...) 6. └─dplyr:::lazy_defunct("mutate") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) Execution halted Package: eesim Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘eesim.Rmd’ using rmarkdown Quitting from eesim.Rmd:34-50 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- Backtrace: ▆ 1. ├─... %>% ggplot(aes(x = date, y = value)) 2. ├─ggplot2::ggplot(., aes(x = date, y = value)) 3. ├─tidyr::gather(., variable, value, -date) 4. ├─dplyr::rename(., `Cardiovascular deaths` = cvd, `Ozone concentration (ppb)` = o3) 5. ├─dplyr::select(., date, cvd, o3) 6. ├─dplyr::filter(., year >= 1996) 7. └─dplyr::tbl_df(.) 8. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 9. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'eesim.Rmd' failed with diagnostics: `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- failed re-building ‘eesim.Rmd’ SUMMARY: processing the following file failed: ‘eesim.Rmd’ Error: Vignette re-building failed. Execution halted Package: efdm Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘example.Rmd’ using rmarkdown Quitting from example.Rmd:316-332 [unnamed-chunk-18] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `summarize()`: ℹ In argument: `data.frame(...)`. ℹ In group 1: `region = "Middle"`, `sp0 = "other"`, `vol0 = 1`, `age0 = 1`. Caused by error: ! `data.frame(...)` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─... %>% ... 2. ├─dplyr::summarize(...) 3. ├─dplyr:::summarise.grouped_df(...) 4. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 5. │ └─base::withCallingHandlers(...) 6. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'example.Rmd' failed with diagnostics: ℹ In argument: `data.frame(...)`. ℹ In group 1: `region = "Middle"`, `sp0 = "other"`, `vol0 = 1`, `age0 = 1`. Caused by error: ! `data.frame(...)` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘example.Rmd’ SUMMARY: processing the following file failed: ‘example.Rmd’ Error: Vignette re-building failed. Execution halted Package: eHDPrep Check: examples New result: ERROR Running examples in ‘eHDPrep-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: apply_quality_ctrl > ### Title: Apply quality control measures to a dataset > ### Aliases: apply_quality_ctrl > > ### ** Examples > > data(example_data) > require(tibble) Loading required package: tibble > > # create an example class_tbl object > # note that diabetes_type is classes as ordinal and is not modified as its > # levels are not pre-coded > tibble::tribble(~"var", ~"datatype", + "patient_id", "id", + "tumoursize", "numeric", + "t_stage", "ordinal_tstage", + "n_stage", "ordinal_nstage", + "diabetes", "factor", + "diabetes_type", "ordinal", + "hypertension", "factor", + "rural_urban", "factor", + "marital_status", "factor", + "SNP_a", "genotype", + "SNP_b", "genotype", + "free_text", "freetext") -> data_types > > data_QC <- apply_quality_ctrl(example_data, patient_id, data_types, + bin_cats =c("No" = "Yes", "rural" = "urban"), min_freq = 0.6) Error in `dplyr::summarise()`: ℹ In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`. Caused by error: ! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1, not 1000. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─eHDPrep::apply_quality_ctrl(...) 2. │ └─... %>% suppressWarnings() 3. ├─base::suppressWarnings(.) 4. │ └─base::withCallingHandlers(...) 5. ├─eHDPrep::encode_cats(...) 6. │ └─dplyr::select(data, !!!dplyr::enquos(...)) 7. ├─base::suppressMessages(.) 8. │ └─base::withCallingHandlers(...) 9. ├─eHDPrep::encode_genotypes(...) 10. │ └─data %>% ... 11. ├─dplyr::mutate(., dplyr::across(c(!!!vars), encode_genotype_vec)) 12. ├─eHDPrep::encode_ordinals(...) 13. │ └─... %>% dplyr::filter(.data$value > 0) 14. ├─dplyr::filter(., .data$value > 0) 15. ├─tidyr::pivot_longer(., dplyr::everything()) 16. ├─dplyr::summarise(., dplyr::across(c(!!!vars), sum)) 17. ├─dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels)) 18. ├─dplyr::select(., !!!vars) 19. ├─eHDPrep::encode_ordinals(...) 20. │ └─... %>% dplyr::filter(.data$value > 0) 21. ├─dplyr::filter(., .data$value > 0) 22. ├─tidyr::pivot_longer(., dplyr::everything()) 23. ├─dplyr::summarise(., dplyr::across(c(!!!vars), sum)) 24. ├─dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels)) 25. ├─dplyr:::summarise.data.frame(., dplyr::across(everything(), ~!.x %in% ord_levels)) 26. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 27. │ └─base::withCallingHandlers(...) 28. ├─dplyr:::dplyr_internal_error(...) 29. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 30. │ └─rlang:::signal_abort(cnd, .file) 31. │ └─base::signalCondition(cnd) 32. └─dplyr (local) ``(``) 33. └─dplyr (local) handler(cnd) 34. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: eHDPrep Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown Quitting from Introduction_to_eHDPrep.Rmd:245-252 [unnamed-chunk-14] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarise()`: i In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`. Caused by error: ! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1, not 1000. i To return more or less than 1 row per group, use `reframe()`. --- Backtrace: x 1. +-eHDPrep::apply_quality_ctrl(...) 2. | \-... %>% suppressWarnings() 3. +-base::suppressWarnings(.) 4. | \-base::withCallingHandlers(...) 5. +-eHDPrep::encode_cats(...) 6. | \-dplyr::select(data, !!!dplyr::enquos(...)) 7. +-base::suppressMessages(.) 8. | \-base::withCallingHandlers(...) 9. +-eHDPrep::encode_genotypes(...) 10. | \-data %>% ... 11. +-dplyr::mutate(., dplyr::across(c(!!!vars), encode_genotype_vec)) 12. +-eHDPrep::encode_ordinals(...) 13. | \-... %>% dplyr::filter(.data$value > 0) 14. +-dplyr::filter(., .data$value > 0) 15. +-tidyr::pivot_longer(., dplyr::everything()) 16. +-dplyr::summarise(., dplyr::across(c(!!!vars), sum)) 17. +-dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels)) 18. +-dplyr::select(., !!!vars) 19. +-eHDPrep::encode_ordinals(...) 20. | \-... %>% dplyr::filter(.data$value > 0) 21. +-dplyr::filter(., .data$value > 0) 22. +-tidyr::pivot_longer(., dplyr::everything()) 23. +-dplyr::summarise(., dplyr::across(c(!!!vars), sum)) 24. +-dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels)) 25. +-dplyr:::summarise.data.frame(., dplyr::across(everything(), ~!.x %in% ord_levels)) 26. | \-dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 27. | \-base::withCallingHandlers(...) 28. \-dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics: ℹ In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`. Caused by error: ! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1, not 1000. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘Introduction_to_eHDPrep.Rmd’ SUMMARY: processing the following file failed: ‘Introduction_to_eHDPrep.Rmd’ Error: Vignette re-building failed. Execution halted Package: eider Check: R code for possible problems New result: NOTE featurise_count: no visible binding for global variable ‘id’ featurise_present: no visible binding for global variable ‘id’ featurise_summary: no visible binding for global variable ‘id’ featurise_time_since: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: eoffice Check: examples New result: ERROR Running examples in ‘eoffice-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: indocx > ### Title: read table from docx > ### Aliases: indocx > > ### ** Examples > > totable(t.test(wt ~ am, mtcars), filename = file.path(tempdir(), "mtcars.docx")) > tabs <- indocx(filename = file.path(tempdir(), "mtcars.docx"), header = TRUE) Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. └─eoffice::indocx(...) 2. └─eoffice::inoffice(filename, format = "docx", header = header) 3. └─dplyr::filter_(content, ~content_type %in% "table cell") 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: eoffice Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘eoffice.Rmd’ using knitr Quitting from eoffice.Rmd:62-94 [fig2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. └─eoffice::inpptx(...) 2. └─eoffice::inoffice(filename, format = "pptx", header = header) 3. └─dplyr::filter_(content, ~content_type %in% "table cell") 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'eoffice.Rmd' failed with diagnostics: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘eoffice.Rmd’ SUMMARY: processing the following file failed: ‘eoffice.Rmd’ Error: Vignette re-building failed. Execution halted Package: EpiSignalDetection Check: examples New result: ERROR Running examples in ‘EpiSignalDetection-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: aggAtlasExport > ### Title: Aggregate filtered final Atlas export > ### Aliases: aggAtlasExport > > ### ** Examples > > #-- Setting the parameters to run the report for > input <- list( + disease = "Salmonellosis", + country = "EU-EEA - complete series", + indicator = "Reported cases", + stratification = "Confirmed cases", + unit = "Month", + daterange = c("2010-01-01", "2016-12-31"), + algo = "FarringtonFlexible", + testingperiod = 5 + ) > > #-- Example dataset > dataset <- EpiSignalDetection::SignalData > > #-- Filtering on declared input parameters > dataset <- filterAtlasExport(dataset, input) > > #-- Aggregating the data by geographical level and time point > dataset <- aggAtlasExport(dataset, input) Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. └─EpiSignalDetection::aggAtlasExport(dataset, input) 2. └─dplyr::group_by_(x, c("StudyPeriod")) 3. └─dplyr:::lazy_defunct("group_by") 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Package: EpiSignalDetection Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘EpiSignalDetection_Vignette.Rmd’ using rmarkdown Quitting from EpiSignalDetection_Vignette.Rmd:179-191 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. └─dplyr::group_by_(my_dataset, c("Population")) 2. └─dplyr:::lazy_defunct("group_by") 3. └─lifecycle::deprecate_stop(...) 4. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EpiSignalDetection_Vignette.Rmd' failed with diagnostics: `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘EpiSignalDetection_Vignette.Rmd’ SUMMARY: processing the following file failed: ‘EpiSignalDetection_Vignette.Rmd’ Error: Vignette re-building failed. Execution halted Package: eq5dsuite Check: R code for possible problems New result: NOTE .pchctab: no visible binding for global variable ‘id’ table_1_2_4: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: estadistica Check: R code for possible problems New result: NOTE regresion.simple: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: etl Check: R code for possible problems New result: NOTE etl_transform.etl_cities: no visible binding for global variable ‘location’ Undefined global functions or variables: location Package: etl Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'etl.Rd': ‘[dplyr:src_dbi]{dplyr::src_dbi()}’ Missing link(s) in Rd file 'src_mysql_cnf.Rd': ‘[dplyr:src_dbi]{dplyr::src_mysql()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: evanverse Check: tests New result: ERROR Running ‘testthat.R’ [39s/39s] 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(evanverse) > > test_check("evanverse") x RDS file not found: '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d2619a85b.rds' v Installed: stats v Installed: cli v Installed: ggplot2 v Installed: stats v Installed: utils -- Compiling Color Palettes (JSON \u2192 RDS) ---------------------------------- v Added 'demo_palette' (Type: qualitative, 2 colors) v Saved RDS: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d47217e9e.rds -- Compilation Summary -- i Sequential: 0 i Diverging: 0 i Qualitative: 1 v All palettes compiled successfully! -- Compiling Color Palettes (JSON \u2192 RDS) ---------------------------------- ! Failed to parse JSON: /home/hornik/tmp/scratch/RtmpSJs3Ne/palettes_15446d7d2dc581/qualitative/invalid.json v Saved RDS: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d41fa6719.rds -- Compilation Summary -- i Sequential: 0 i Diverging: 0 i Qualitative: 0 v All palettes compiled successfully! -- Compiling Color Palettes (JSON \u2192 RDS) ---------------------------------- ! Missing fields (colors) in: /home/hornik/tmp/scratch/RtmpSJs3Ne/palettes_15446d3339325d/qualitative/incomplete.json v Saved RDS: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d23099e.rds -- Compilation Summary -- i Sequential: 0 i Diverging: 0 i Qualitative: 0 v All palettes compiled successfully! -- Compiling Color Palettes (JSON \u2192 RDS) ---------------------------------- v Added 'seq_pal' (Type: sequential, 2 colors) v Added 'div_pal' (Type: diverging, 2 colors) v Saved RDS: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d31de629f.rds -- Compilation Summary -- i Sequential: 1 i Diverging: 1 i Qualitative: 0 v All palettes compiled successfully! i Converting symbols to UPPERCASE (human standard) i Creating standardized column: symbol_upper i Creating standardized column: symbol_lower i Converting symbols to UPPERCASE (human standard) i Converting symbols to UPPERCASE (human standard) i Directory created: /home/hornik/tmp/scratch/RtmpSJs3Ne/palette_test_15446d338dadc4/qualitative v Palette saved: /home/hornik/tmp/scratch/RtmpSJs3Ne/palette_test_15446d338dadc4/qualitative/testset.json i Directory created: /home/hornik/tmp/scratch/RtmpSJs3Ne/reuse_test_15446d40cd3e69/diverging v Palette saved: /home/hornik/tmp/scratch/RtmpSJs3Ne/reuse_test_15446d40cd3e69/diverging/reused.json ! Palette already exists: /home/hornik/tmp/scratch/RtmpSJs3Ne/reuse_test_15446d40cd3e69/diverging/reused.json i Directory created: /home/hornik/tmp/scratch/RtmpSJs3Ne/log_test_15446d3d248898/qualitative v Palette saved: /home/hornik/tmp/scratch/RtmpSJs3Ne/log_test_15446d3d248898/qualitative/logtest.json -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d2aa3ddc2 ------ +-- test.txt -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d3d2df6d7 ------ +-- file1.txt +-- subdir +-- file2.txt -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446dc7162be ------- +-- level1 -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446dc7162be ------- +-- level1 +-- level2 +-- deep_file.txt -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d30b8e47c ------ +-- example.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d30b8e47c/logs/tree/test.log -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d38f48d91 ------ +-- sample.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d38f48d91/logs/content_test.log -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d66d642ac ------ +-- test.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d66d642ac/logs/file_tree_20260201_180633.log -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d384d07d6 ------ +-- file1.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d6da57aa7/overwrite_test.log -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d384d07d6 ------ +-- file1.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d6da57aa7/overwrite_test.log -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d2fab72d9 ------ +-- file1.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d34f2e22c/append_test.log -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d2fab72d9 ------ +-- file1.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d34f2e22c/append_test.log x Directory does not exist: nonexistent/directory/path -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d6d79b03 ------- -- Directory Tree: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d7788df09 ------ +-- test.txt v File tree log saved to: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d7788df09/new/log/path/test.log v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors i #FF8000 -> RGB: c(255, 128, 0) i #00FF00 -> RGB: c(0, 255, 0) i Mapping completed for 'id': 1 unmatched value(s) assigned to default. i Mapping completed for 'id': 1 unmatched value(s) assigned to default. i Mapping completed for 'group': 1 unmatched value(s) assigned to default. i Mapping completed for 'id': 1 unmatched value(s) assigned to default. -- Objects are NOT identical --------------------------------------------------- x Type mismatch: integer vs double x Class mismatch: integer vs numeric x Values differ at 1 position(s), e.g., index 3: 3 vs 4 -- Objects are NOT identical --------------------------------------------------- x Values differ at 1 position(s), e.g., index 2: b vs c -- Objects are NOT identical --------------------------------------------------- x Type mismatch: integer vs double x Values differ at 1 cell(s), e.g., [2,2]: 4 vs 5 -- Objects are NOT identical --------------------------------------------------- x Values differ in column 'y' at 1 row(s), e.g., row 2: b vs c -- Objects are NOT identical --------------------------------------------------- x Names differ: a, b vs b, a x Values differ at 2 position(s), e.g., index 1: 1 vs 2 -- Objects are NOT identical --------------------------------------------------- x Column names differ: x, y vs y, x -- Objects are NOT identical --------------------------------------------------- x Dimnames differ: (r1|r2; c1|c2) vs (r1|r2; cX|c2) -- Objects are NOT identical --------------------------------------------------- -- Objects are NOT identical --------------------------------------------------- -- Objects are NOT identical --------------------------------------------------- x Dimension mismatch: 0x0 vs 1x0 -- Objects are NOT identical --------------------------------------------------- x Length mismatch: 2 vs 3 -- Objects are NOT identical --------------------------------------------------- x Dimension mismatch: 2x2 vs 1x4 -- Objects are NOT identical --------------------------------------------------- x Column names differ: x vs y x Unsupported type for 'a': list x Unsupported type for 'b': function ! Large n (25) may cause numeric overflow. Consider using the 'gmp' package for arbitrary precision. ! Large n (171) may cause numeric overflow. Consider using the 'gmp' package for arbitrary precision. -- Package: stats -- i Matched exported names: 461 .MFclass .checkMFClasses .getXlevels .lm.fit .nknots.smspl .preformat.ts .vcov.aliased AIC ARMAacf ARMAtoMA BIC Box.test C D DF2formula Gamma HoltWinters IQR KalmanForecast KalmanLike KalmanRun KalmanSmooth NLSstAsymptotic NLSstClosestX NLSstLfAsymptote NLSstRtAsymptote PP.test Pair SSD SSasymp SSasympOff SSasympOrig SSbiexp SSfol SSfpl SSgompertz SSlogis SSmicmen SSweibull StructTS TukeyHSD acf acf2AR add.scope add1 addmargins aggregate aggregate.data.frame aggregate.ts alias anova ansari.test aov approx approxfun ar ar.burg ar.mle ar.ols ar.yw arima arima.sim arima0 arima0.diag as.dendrogram as.dist as.formula as.hclust as.stepfun as.ts asOneSidedFormula ave bandwidth.kernel bartlett.test binom.test binomial biplot bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv cancor case.names ccf chisq.test cmdscale coef coefficients complete.cases confint confint.default confint.lm constrOptim contr.SAS contr.helmert contr.poly contr.sum contr.treatment contrasts contrasts<- convolve cooks.distance cophenetic cor cor.test cov cov.wt cov2cor covratio cpgram cutree cycle dbeta dbinom dcauchy dchisq decompose delete.response deltat dendrapply density density.default deriv deriv3 deviance dexp df df.kernel df.residual dfbeta dfbetas dffits dgamma dgeom dhyper diffinv dist dlnorm dlogis dmultinom dnbinom dnorm dpois drop.scope drop.terms drop1 dsignrank dt dummy.coef dummy.coef.lm dunif dweibull dwilcox ecdf eff.aovlist effects embed end estVar expand.model.frame extractAIC factanal factor.scope family fft filter fisher.test fitted fitted.values fivenum fligner.test formula frequency friedman.test ftable gaussian getCall getInitial get_all_vars glm glm.control glm.fit hasTsp hat hatvalues hclust heatmap influence influence.measures integrate interaction.plot inverse.gaussian is.empty.model is.leaf is.mts is.stepfun is.ts is.tskernel isoreg kernapply kernel kmeans knots kruskal.test ks.test ksmooth lag lag.plot line lm lm.fit lm.influence lm.wfit loadings loess loess.control loess.smooth logLik loglin lowess ls.diag ls.print lsfit mad mahalanobis make.link makeARIMA makepredictcall manova mantelhaen.test mauchly.test mcnemar.test median median.default medpolish model.extract model.frame model.frame.default model.matrix model.matrix.default model.matrix.lm model.offset model.response model.tables model.weights monthplot mood.test mvfft na.action na.contiguous na.exclude na.fail na.omit na.pass napredict naprint naresid nextn nlm nlminb nls nls.control nobs numericDeriv offset oneway.test optim optimHess optimise optimize order.dendrogram p.adjust p.adjust.methods pacf pairwise.prop.test pairwise.t.test pairwise.table pairwise.wilcox.test pbeta pbinom pbirthday pcauchy pchisq pexp pf pgamma pgeom phyper plclust plnorm plogis plot.ecdf plot.spec.coherency plot.spec.phase plot.stepfun plot.ts pnbinom pnorm poisson poisson.test poly polym power power.anova.test power.prop.test power.t.test ppoints ppois ppr prcomp predict predict.glm predict.lm preplot princomp printCoefmat profile proj promax prop.test prop.trend.test psignrank psmirnov pt ptukey punif pweibull pwilcox qbeta qbinom qbirthday qcauchy qchisq qexp qf qgamma qgeom qhyper qlnorm qlogis qnbinom qnorm qpois qqline qqnorm qqplot qr.influence qsignrank qsmirnov qt qtukey quade.test quantile quasi quasibinomial quasipoisson qunif qweibull qwilcox r2dtable rWishart rbeta rbinom rcauchy rchisq read.ftable rect.hclust reformulate relevel reorder replications reshape resid residuals residuals.glm residuals.lm rexp rf rgamma rgeom rhyper rlnorm rlogis rmultinom rnbinom rnorm rpois rsignrank rsmirnov rstandard rstudent rt runif runmed rweibull rwilcox scatter.smooth screeplot sd se.contrast selfStart setNames shapiro.test sigma simulate smooth smooth.spline smoothEnds sortedXyData spec.ar spec.pgram spec.taper spectrum spline splinefun splinefunH start stat.anova step stepfun stl summary.aov summary.glm summary.lm summary.manova summary.stepfun supsmu symnum t.test termplot terms terms.formula time toeplitz toeplitz2 ts ts.intersect ts.plot ts.union tsSmooth tsdiag tsp tsp<- uniroot update update.default update.formula var var.test variable.names varimax vcov weighted.mean weighted.residuals weights wilcox.test window window<- write.ftable xtabs -- Package: stats -- i Matched exported names: 461 .MFclass .checkMFClasses .getXlevels .lm.fit .nknots.smspl .preformat.ts .vcov.aliased AIC ARMAacf ARMAtoMA BIC Box.test C D DF2formula Gamma HoltWinters IQR KalmanForecast KalmanLike KalmanRun KalmanSmooth NLSstAsymptotic NLSstClosestX NLSstLfAsymptote NLSstRtAsymptote PP.test Pair SSD SSasymp SSasympOff SSasympOrig SSbiexp SSfol SSfpl SSgompertz SSlogis SSmicmen SSweibull StructTS TukeyHSD acf acf2AR add.scope add1 addmargins aggregate aggregate.data.frame aggregate.ts alias anova ansari.test aov approx approxfun ar ar.burg ar.mle ar.ols ar.yw arima arima.sim arima0 arima0.diag as.dendrogram as.dist as.formula as.hclust as.stepfun as.ts asOneSidedFormula ave bandwidth.kernel bartlett.test binom.test binomial biplot bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv cancor case.names ccf chisq.test cmdscale coef coefficients complete.cases confint confint.default confint.lm constrOptim contr.SAS contr.helmert contr.poly contr.sum contr.treatment contrasts contrasts<- convolve cooks.distance cophenetic cor cor.test cov cov.wt cov2cor covratio cpgram cutree cycle dbeta dbinom dcauchy dchisq decompose delete.response deltat dendrapply density density.default deriv deriv3 deviance dexp df df.kernel df.residual dfbeta dfbetas dffits dgamma dgeom dhyper diffinv dist dlnorm dlogis dmultinom dnbinom dnorm dpois drop.scope drop.terms drop1 dsignrank dt dummy.coef dummy.coef.lm dunif dweibull dwilcox ecdf eff.aovlist effects embed end estVar expand.model.frame extractAIC factanal factor.scope family fft filter fisher.test fitted fitted.values fivenum fligner.test formula frequency friedman.test ftable gaussian getCall getInitial get_all_vars glm glm.control glm.fit hasTsp hat hatvalues hclust heatmap influence influence.measures integrate interaction.plot inverse.gaussian is.empty.model is.leaf is.mts is.stepfun is.ts is.tskernel isoreg kernapply kernel kmeans knots kruskal.test ks.test ksmooth lag lag.plot line lm lm.fit lm.influence lm.wfit loadings loess loess.control loess.smooth logLik loglin lowess ls.diag ls.print lsfit mad mahalanobis make.link makeARIMA makepredictcall manova mantelhaen.test mauchly.test mcnemar.test median median.default medpolish model.extract model.frame model.frame.default model.matrix model.matrix.default model.matrix.lm model.offset model.response model.tables model.weights monthplot mood.test mvfft na.action na.contiguous na.exclude na.fail na.omit na.pass napredict naprint naresid nextn nlm nlminb nls nls.control nobs numericDeriv offset oneway.test optim optimHess optimise optimize order.dendrogram p.adjust p.adjust.methods pacf pairwise.prop.test pairwise.t.test pairwise.table pairwise.wilcox.test pbeta pbinom pbirthday pcauchy pchisq pexp pf pgamma pgeom phyper plclust plnorm plogis plot.ecdf plot.spec.coherency plot.spec.phase plot.stepfun plot.ts pnbinom pnorm poisson poisson.test poly polym power power.anova.test power.prop.test power.t.test ppoints ppois ppr prcomp predict predict.glm predict.lm preplot princomp printCoefmat profile proj promax prop.test prop.trend.test psignrank psmirnov pt ptukey punif pweibull pwilcox qbeta qbinom qbirthday qcauchy qchisq qexp qf qgamma qgeom qhyper qlnorm qlogis qnbinom qnorm qpois qqline qqnorm qqplot qr.influence qsignrank qsmirnov qt qtukey quade.test quantile quasi quasibinomial quasipoisson qunif qweibull qwilcox r2dtable rWishart rbeta rbinom rcauchy rchisq read.ftable rect.hclust reformulate relevel reorder replications reshape resid residuals residuals.glm residuals.lm rexp rf rgamma rgeom rhyper rlnorm rlogis rmultinom rnbinom rnorm rpois rsignrank rsmirnov rstandard rstudent rt runif runmed rweibull rwilcox scatter.smooth screeplot sd se.contrast selfStart setNames shapiro.test sigma simulate smooth smooth.spline smoothEnds sortedXyData spec.ar spec.pgram spec.taper spectrum spline splinefun splinefunH start stat.anova step stepfun stl summary.aov summary.glm summary.lm summary.manova summary.stepfun supsmu symnum t.test termplot terms terms.formula time toeplitz toeplitz2 ts ts.intersect ts.plot ts.union tsSmooth tsdiag tsp tsp<- uniroot update update.default update.formula var var.test variable.names varimax vcov weighted.mean weighted.residuals weights wilcox.test window window<- write.ftable xtabs -- Package: stats -- i Matched exported names: 24 .lm.fit KalmanForecast KalmanLike KalmanRun KalmanSmooth confint.lm contr.helmert dummy.coef.lm glm glm.control glm.fit lm lm.fit lm.influence lm.wfit model.matrix.lm nlm nlminb predict.glm predict.lm residuals.glm residuals.lm summary.glm summary.lm -- Package: stats -- i Matched exported names: 24 .lm.fit KalmanForecast KalmanLike KalmanRun KalmanSmooth confint.lm contr.helmert dummy.coef.lm glm glm.control glm.fit lm lm.fit lm.influence lm.wfit model.matrix.lm nlm nlminb predict.glm predict.lm residuals.glm residuals.lm summary.glm summary.lm -- Package: stats -- i Matched exported names: 0 ! No exported names matched keyword: zzzzzz Saving _problems/test-plot_pie-69.R Saving _problems/test-plot_pie-75.R Saving _problems/test-plot_pie-97.R Saving _problems/test-plot_pie-97.R Saving _problems/test-plot_pie-97.R Saving _problems/test-plot_pie-97.R Saving _problems/test-plot_pie-135.R Saving _problems/test-plot_pie-146.R i s1 had 74 duplicates, now de-duplicated. i s2 had 94 duplicates, now de-duplicated. i s1 had 74 duplicates, now de-duplicated. i s2 had 94 duplicates, now de-duplicated. i a had 27 duplicates, now de-duplicated. i b had 19 duplicates, now de-duplicated. v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors v Loaded palette "vividset" ("qualitative"), 9 colors -- Reading Excel file -- i Sheets in '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446dceb6fc.xlsx': Sheet1 v Column names cleaned with janitor::clean_names(). v Successfully read sheet 1 from '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446dceb6fc.xlsx'. -- Reading Excel file -- i Sheets in '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d18c7ecb8.xlsx': Sheet1 v Column names cleaned with janitor::clean_names(). v Successfully read sheet 1 from '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d18c7ecb8.xlsx'. -- Reading Excel file -- i Sheets in '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d2629ba51.xlsx': Sheet1 v Successfully read sheet 1 from '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d2629ba51.xlsx'. -- Reading Excel file -- i Sheets in '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d778b886.xlsx': Sheet1 v Column names cleaned with janitor::clean_names(). v Successfully read sheet 1 from '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d778b886.xlsx'. Path: '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d54ee631a.csv' Separator: "," | Encoding: "UTF-8" OpenMP version (_OPENMP) 201511 omp_get_num_procs() 32 R_DATATABLE_NUM_PROCS_PERCENT unset (default 50) R_DATATABLE_NUM_THREADS unset R_DATATABLE_THROTTLE unset (default 1024) omp_get_thread_limit() 3 omp_get_max_threads() 3 OMP_THREAD_LIMIT 3 OMP_NUM_THREADS 3 RestoreAfterFork true data.table is using 3 threads with throttle==1024. See ?setDTthreads. freadR.c has been passed a filename: /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d54ee631a.csv [01] Check arguments Using 3 threads (omp_get_max_threads()=3, nth=3) NAstrings = [<>] None of the NAstrings look like numbers. show progress = 1 0/1 column will be read as integer Y/N column will be read as character [02] Opening the file Opening file /home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d54ee631a.csv File opened, size = 235 bytes. Memory mapped ok [03] Detect and skip BOM [04] Arrange mmap to be \0 terminated \n has been found in the input (counts: 0 \r by themselves vs 6 [\r]*\n) and different lines can end with different line endings (e.g. mixed \n and \r\n in one file). This is common and ideal. [05] Skipping initial rows if needed Positioned on line 1 starting: <> [06] Detect separator, quoting rule, and ncolumns Using supplied sep ',' sep=',' with 6 lines of 11 fields using quote rule 0 Detected 11 columns on line 1. This line is either column names or first data row. Line starts as: <> Quote rule picked = 0 fill=false and the most number of columns found is 11 [07] Detect column types, dec, good nrow estimate and whether first row is column names 'header' changed by user from 'auto' to true sep=',' so dec set to '.' Number of sampling jump points = 1 because (234 bytes from row 1 to eof) / (2 * 234 jump0size) == 0 Type codes (jump 000) : 97779997777 Quote rule 0 All rows were sampled since file is small so we know nrow=5 exactly [08] Assign column names [09] Apply user overrides on column types After 0 type and 0 drop user overrides : 97779997777 [10] Allocate memory for the datatable Allocating 11 column slots (11 - 0 dropped) with 5 rows [11] Read the data jumps=[0..1), chunk_size=1048576, total_size=189 Read 5 rows x 11 columns from 235 bytes file in 00:00.000 wall clock time [12] Finalizing the datatable Type counts: 7 : int32 '7' 4 : float64 '9' ============================= 0.000s ( 37%) Memory map 0.000GiB file 0.000s ( 41%) sep=',' ncol=11 and header detection 0.000s ( 5%) Column type detection using 5 sample rows 0.000s ( 4%) Allocation of 5 rows x 11 cols (0.000GiB) of which 5 (100%) rows used 0.000s ( 12%) Reading 1 chunks (0 swept) of 1.000MiB (each chunk 5 rows) using 1 threads + 0.000s ( 3%) Parse to row-major thread buffers (grown 0 times) + 0.000s ( 1%) Transpose + 0.000s ( 9%) Waiting 0.000s ( 0%) Rereading 0 columns due to out-of-sample type exceptions 0.000s Total v File loaded successfully (5 rows \u00d7 11 cols) -- glimpse `glimpse(df)` from dplyr/tibble gives a compact overview. -- glimpse `glimpse(df)` from dplyr/tibble gives a compact overview. -- read_excel `readxl::read_excel("yourfile.xlsx")` reads Excel files. Supports `sheet =`, `range =`, etc. -- glimpse `glimpse(df)` from dplyr/tibble gives a compact overview. -- Usage Examples -------------------------------------------------------------- -- glimpse `glimpse(df)` from dplyr/tibble gives a compact overview. -- read_excel `readxl::read_excel("yourfile.xlsx")` reads Excel files. Supports `sheet =`, `range =`, etc. -- droplevels `droplevels(df)` removes unused factor levels from a data frame or factor. -- modifyList `modifyList(x, y)` merges two lists; elements in `y` overwrite those in `x`. -- do.call `do.call(fun, args)` calls a function with arguments in a list: `do.call(plot, list(x = 1:10))`. -- sprintf `sprintf("Hello, %s!", name)` formats strings with `%s`, `%d`, etc. -- scRNAseq `scRNAseq` (Bioconductor) provides scRNA-seq datasets, e.g., `ZeiselBrainData()`. -- basename `basename(path)` extracts the filename from a full path. See also `dirname()`. -- here `here::here("data", "raw", "sample1.rds")` builds a path from project root. -- stopifnot `stopifnot(cond1, cond2, ...)` throws if any condition is FALSE. -- object.size `object.size(x)` estimates memory size; use `format()` to pretty-print. -- slice `slice(df, 1:3)` selects rows by position; see `slice_head()`, `slice_tail()`, `slice_max()`. -- unzip `unzip("file.zip", exdir = "dir")` extracts ZIP archives. -- gunzip `R.utils::gunzip("file.csv.gz", remove = FALSE)` decompresses .gz files. -- untar `untar("file.tar.gz", exdir = "dir")` extracts .tar or .tar.gz archives. -- NoLegend `NoLegend()` removes legends from ggplot2/Seurat plots. -- RotatedAxis `RotatedAxis()` rotates x-axis text for readability in dot plots. -- guides `guides(fill = "none")` customizes or removes legends (with `scale_*`). -- log2 `log2(x)` base-2 logarithm (often for fold change). -- log `log(x, base = exp(1))` natural log by default; set `base = 10` or `2` for others. -- log10 `log10(x)` base-10 logarithm (orders of magnitude). -- round `round(x, digits = 0)` rounds; use `signif()` for significant digits. -- floor `floor(x)` greatest integer ≤ x (e.g., `floor(2.8)` -> 2). -- ceiling `ceiling(x)` smallest integer ≥ x (e.g., `ceiling(2.1)` -> 3). -- cut `cut(x, breaks)` bins numeric vector; `breaks = 3` or custom; `labels = FALSE` for group indices. -- cumsum `cumsum(x)` cumulative sum. -- cumprod `cumprod(x)` cumulative product. -- cummin `cummin(x)` running minimum. -- cummax `cummax(x)` running maximum. -- row_number `row_number(x)` order rank (ties broken arbitrarily). -- min_rank `min_rank(x)` ties get the same minimum rank. -- dense_rank `dense_rank(x)` like `min_rank()` but without gaps. -- percent_rank `percent_rank(x)` relative rank in [0,1], normalized by n-1. -- cume_dist `cume_dist(x)` cumulative proportion of values ≤ x. -- str_view `stringr::str_view(string, pattern)` highlights regex matches; `str_view_all()` for all. -- str_c `stringr::str_c(...)` concatenates; use `sep`/`collapse` as needed. -- str_glue `glue::glue("Hello, {name}!")` inline expressions with `{}`. -- str_flatten `stringr::str_flatten(x, collapse = ", ")` join a character vector. -- str_length `stringr::str_length(x)` string lengths. -- str_sub `stringr::str_sub(x, start, end)` extract/replace substrings (supports negative indices). -- today `lubridate::today()` current Date (no time). -- now `lubridate::now()` current POSIXct date-time. -- Sys.timezone `Sys.timezone()` system time zone name. -- skimr `skimr::skim(df)` compact, readable data summaries. -- par `par(mfrow = c(m, n))` split plotting area (e.g., 2x2). -- layout `layout(matrix, widths, heights)` flexible plot arrangement. -- datatable `DT::datatable(data)` interactive table (search/filter/sort/paginate). -- windowsFonts `windowsFonts()` register system fonts (Windows). -- sign `sign(x)` returns -1/0/1 for negative/zero/positive. -- reactable `reactable::reactable(data)` modern interactive table. -- trimws `trimws(x)` removes leading and trailing whitespace. -- Available Keywords ---------------------------------------------------------- `glimpse, read_excel, droplevels, modifyList, do.call, sprintf, scRNAseq, basename, here, stopifnot, object.size, slice, unzip, gunzip, untar, NoLegend, RotatedAxis, guides, log2, log, log10, round, floor, ceiling, cut, cumsum, cumprod, cummin, cummax, row_number, min_rank, dense_rank, percent_rank, cume_dist, str_view, str_c, str_glue, str_flatten, str_length, str_sub, today, now, Sys.timezone, skimr, par, layout, datatable, windowsFonts, sign, reactable, trimws` x No match found for keyword: "notakeyword" -- min_rank `min_rank(x)` ties get the same minimum rank. -- dense_rank `dense_rank(x)` like `min_rank()` but without gaps. -- percent_rank `percent_rank(x)` relative rank in [0,1], normalized by n-1. v Palette removed from qualitative: '/home/hornik/tmp/scratch/RtmpSJs3Ne/palettes_test_15446d7e31909c/qualitative/test_palette.json' ! Palette not found in any type: nonexistent v Palette removed from diverging: '/home/hornik/tmp/scratch/RtmpSJs3Ne/palettes_test_15446d2c19c05a/diverging/test_palette.json' v Palette removed from qualitative: '/home/hornik/tmp/scratch/RtmpSJs3Ne/custom_palettes_15446d5c5ea27b/qualitative/custom_test.json' v RGB: c(255, 128, 0) → HEX: #FF8000 v RGB: c(0, 0, 0) → HEX: #000000 v RGB: c(255, 255, 255) → HEX: #FFFFFF v Converted 3 RGB values to HEX. i RGB: c(255, 128, 0) → HEX: #FF8000 i RGB: c(0, 255, 0) → HEX: #00FF00 i RGB: c(0, 0, 255) → HEX: #0000FF v RGB: c(0, 1, 255) → HEX: #0001FF x An error occurred: non-numeric argument to mathematical function -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting bioc mirror -- v Bioconductor mirror set to: i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting bioc mirror -- v Bioconductor mirror set to: i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting bioc mirror -- v Bioconductor mirror set to: i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting all mirror -- v CRAN mirror set to: v Bioconductor mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting all mirror -- v CRAN mirror set to: v Bioconductor mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting cran mirror -- -- Setting bioc mirror -- -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting all mirror -- v CRAN mirror set to: v Bioconductor mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting cran mirror -- i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting bioc mirror -- i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting cran mirror -- v CRAN mirror set to: i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting bioc mirror -- -- Setting all mirror -- -- Setting cran mirror -- v CRAN mirror set to: i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` -- Setting bioc mirror -- v Bioconductor mirror set to: i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju" i View current settings: `getOption('repos')` & `getOption('BioC_mirror')` i Square test started at 2026-02-01 18:06:58 v Square test completed in 0.000 seconds i Silent task started at 2026-02-01 18:06:58 v Silent task completed in 0.000 seconds v Excel file written to '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d7272abea.xlsx' v Excel file written to '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d5604d2b.xlsx' v Excel file written to '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d6e05045e.xlsx' ! File already exists and will be overwritten: '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d6e05045e.xlsx' v Excel file written to '/home/hornik/tmp/scratch/RtmpSJs3Ne/file15446d6e05045e.xlsx' v Excel file written to '/home/hornik/tmp/scratch/RtmpSJs3Ne/test-write-15446d5a6e4461_2026-02-01.xlsx' [ FAIL 8 | WARN 5 | SKIP 44 | PASS 1310 ] ══ Skipped tests (44) ══════════════════════════════════════════════════════════ • On CRAN (44): 'test-check_pkg.R:48:3', 'test-download_batch.R:19:3', 'test-download_batch.R:39:3', 'test-download_gene_ref.R:20:3', 'test-download_gene_ref.R:31:3', 'test-download_gene_ref.R:42:3', 'test-download_gene_ref.R:55:3', 'test-download_geo_data.R:11:3', 'test-download_geo_data.R:21:3', 'test-download_geo_data.R:50:3', 'test-download_geo_data.R:61:3', 'test-download_geo_data.R:80:3', 'test-download_geo_data.R:101:3', 'test-download_geo_data.R:155:3', 'test-download_geo_data.R:178:3', 'test-download_geo_data.R:208:3', 'test-download_url.R:10:3', 'test-download_url.R:22:3', 'test-download_url.R:39:3', 'test-download_url.R:103:3', 'test-download_url.R:117:3', 'test-download_url.R:147:3', 'test-download_url.R:177:3', 'test-download_url.R:205:3', 'test-download_url.R:227:3', 'test-download_url.R:252:3', 'test-download_url.R:279:3', 'test-download_url.R:306:3', 'test-file_info.R:12:3', 'test-file_info.R:26:3', 'test-file_info.R:48:3', 'test-file_info.R:59:3', 'test-file_info.R:71:3', 'test-pkg_version.R:19:3', 'test-pkg_version.R:27:3', 'test-pkg_version.R:37:3', 'test-pkg_version.R:48:3', 'test-plot_forest.R:11:3', 'test-plot_forest.R:32:3', 'test-plot_forest.R:53:3', 'test-plot_forest.R:71:3', 'test-plot_forest.R:93:3', 'test-plot_forest.R:119:3', 'test-plot_forest.R:140:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plot_pie.R:69:3'): plot_pie() works with character vector input ── Expected `p <- plot_pie(vec, preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:75:3'): plot_pie() works with data.frame input ──── Expected `p <- plot_pie(df, group_col = "group", count_col = "count", preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ── Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ── Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ── Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ── Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:135:3'): plot_pie() handles custom colors ───────── Expected `p <- plot_pie(df, fill = custom_colors, preview = FALSE)` to run silently. Actual noise: warnings. ── Failure ('test-plot_pie.R:141:3'): plot_pie() handles custom title and colors ── Expected `... <- NULL` to run silently. Actual noise: warnings. [ FAIL 8 | WARN 5 | SKIP 44 | PASS 1310 ] Error: ! Test failures. Execution halted Package: ezec Check: examples New result: ERROR Running examples in ‘ezec-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: EC_table > ### Title: Function to generate a table of EC values from a data frame of > ### multiple isolates. > ### Aliases: EC_table > > ### ** Examples > > data(dummydata) > # Using 3 parameter Log-Logistic Model (default) > EC_table(dummydata, form = response ~ dose) Error: ! `do_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `do()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─ezec::EC_table(dummydata, form = response ~ dose) 2. │ └─dat %>% dplyr::group_by_(idcol) %>% ... 3. └─dplyr::do_(...) 4. └─dplyr:::lazy_defunct("do") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: ezec Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘getting_started.Rmd’ using rmarkdown Quitting from getting_started.Rmd:76-81 [ec_table] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `do_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `do()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─ezec::EC_table(dummydata, form = response ~ dose) 2. │ └─dat %>% dplyr::group_by_(idcol) %>% ... 3. └─dplyr::do_(...) 4. └─dplyr:::lazy_defunct("do") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'getting_started.Rmd' failed with diagnostics: `do_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `do()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘getting_started.Rmd’ SUMMARY: processing the following file failed: ‘getting_started.Rmd’ Error: Vignette re-building failed. Execution halted Package: ezec Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ezec) > > test_check("ezec") Saving _problems/test-tables-45.R [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tables.R:19:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-tables.R:45:3'): EC_table can read files ─────────────────────── Error: `do_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `do()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─ezec::EC_table(tmp, form = response ~ dose, sep = ",") at test-tables.R:45:3 2. │ └─dat %>% dplyr::group_by_(idcol) %>% ... 3. └─dplyr::do_(...) 4. └─dplyr:::lazy_defunct("do") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test-tables.R:54:3'): Insufficient data is handled well ───────────── Error: `do_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `do()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─testthat::expect_output(...) at test-tables.R:54:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─testthat::capture_output_lines(code, print, width = width) 5. │ │ └─testthat:::eval_with_output(code, print = print, width = width) 6. │ │ ├─withr::with_output_sink(path, withVisible(code)) 7. │ │ │ └─base::force(code) 8. │ │ └─base::withVisible(code) 9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 10. ├─ezec::EC_table(...) 11. │ └─dat %>% dplyr::group_by_(idcol) %>% ... 12. └─dplyr::do_(...) 13. └─dplyr:::lazy_defunct("do") 14. └─lifecycle::deprecate_stop(...) 15. └─lifecycle:::deprecate_stop0(msg) 16. └─rlang::cnd_signal(...) [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2 ] Error: ! Test failures. Execution halted Package: faersquarterlydata Check: examples New result: ERROR Running examples in ‘faersquarterlydata-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: unify_tabular_ascii > ### Title: Unify the list to a tabular format > ### Aliases: unify_tabular_ascii > > ### ** Examples > > unify_tabular_ascii(ascii_list = als_faers_data) Error in `summarise()`: ℹ In argument: `indi_pt_ps = sort(unique(indi_pt))`. ℹ In group 79: `primaryid = 129433992`, `caseid = 12943399`. Caused by error: ! `indi_pt_ps` must be size 1, not 0. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─faersquarterlydata::unify_tabular_ascii(ascii_list = als_faers_data) 2. │ └─... %>% relocate(age_YR, .after = "age") 3. ├─dplyr::relocate(., age_YR, .after = "age") 4. ├─dplyr::mutate(...) 5. ├─dplyr::left_join(...) 6. ├─dplyr:::left_join.data.frame(...) 7. │ └─dplyr::auto_copy(x, y, copy = copy) 8. │ ├─dplyr::same_src(x, y) 9. │ └─dplyr:::same_src.data.frame(x, y) 10. │ └─base::is.data.frame(y) 11. ├─... %>% suppressWarnings() 12. ├─base::suppressWarnings(.) 13. │ └─base::withCallingHandlers(...) 14. ├─dplyr::ungroup(.) 15. ├─dplyr::summarise(...) 16. ├─dplyr:::summarise.grouped_df(...) 17. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 18. │ └─base::withCallingHandlers(...) 19. ├─dplyr:::dplyr_internal_error(...) 20. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 21. │ └─rlang:::signal_abort(cnd, .file) 22. │ └─base::signalCondition(cnd) 23. └─dplyr (local) ``(``) 24. └─dplyr (local) handler(cnd) 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: faersquarterlydata Check: tests New result: ERROR Running ‘testthat.R’ [50s/51s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(faersquarterlydata) > > test_check("faersquarterlydata") Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 saving resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 saving resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 saving resources/test_zip_ex_dir/ASCII/INDI22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 saving resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 saving resources/test_zip_ex_dir/ASCII/REAC22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 saving resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt into cache: resources/cache/cache_test.rdata binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 saving resources/test_zip_ex_dir/ASCII/THER22Q4.txt into cache: resources/cache/cache_test.rdata Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 Saving _problems/test-read_func_ascii-51.R retrieving resources/1_ADR22Q1_example.xml retrieving resources/1_ADR22Q1_example.xml retrieving resources/1_ADR22Q1_example.xml retrieving resources/1_ADR22Q1_example.xml retrieving resources/1_ADR22Q1_example.xml 1 out of 1 retrieving resources/1_ADR22Q1_example.xml 1 out of 1 retrieving resources/1_ADR22Q1_example.xml saving resources/1_ADR22Q1_example.xml into cache: resources/cache/cache_xml.Rdata 1 out of 1 retrieving resources/1_ADR22Q1_example.xml Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 Saving _problems/test-ror-23.R Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 1 out of 2 Retrieving drug/indication information: binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 2 out of 2 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4.txt 1 out of 8 binding resources/test_zip_ex_dir/ASCII/DEMO22Q4_test.txt 2 out of 8 binding resources/test_zip_ex_dir/ASCII/DRUG22Q4.txt 3 out of 8 binding resources/test_zip_ex_dir/ASCII/INDI22Q4.txt 4 out of 8 binding resources/test_zip_ex_dir/ASCII/OUTC22Q4.txt 5 out of 8 binding resources/test_zip_ex_dir/ASCII/REAC22Q4.txt 6 out of 8 binding resources/test_zip_ex_dir/ASCII/RPSR22Q4.txt 7 out of 8 binding resources/test_zip_ex_dir/ASCII/THER22Q4.txt 8 out of 8 Saving _problems/test-summary-4.R unzipping resources/xml_files/faers_xml_2012q4.zip unzipping resources/ascii_files//faers_ascii_2022Q4.zip [ FAIL 3 | WARN 36 | SKIP 0 | PASS 37 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-read_func_ascii.R:51:3'): unify_tabular_ascii ────────────────── Error in `summarise(., indi_pt_ps = sort(unique(indi_pt)), drugname_ps = paste(sort(unique(drugname)), collapse = " + "), start_dt_ps = unique(start_dt), .groups = "keep")`: i In argument: `indi_pt_ps = sort(unique(indi_pt))`. i In group 1: `primaryid = 100115733`, `caseid = 10011573`. Caused by error: ! `indi_pt_ps` must be size 1, not 0. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─faersquarterlydata::unify_tabular_ascii(ascii_list = faers_ascii_data) at test-read_func_ascii.R:51:3 2. │ └─... %>% relocate(age_YR, .after = "age") 3. ├─dplyr::relocate(., age_YR, .after = "age") 4. ├─dplyr::mutate(...) 5. ├─dplyr::left_join(...) 6. ├─dplyr:::left_join.data.frame(...) 7. │ └─dplyr::auto_copy(x, y, copy = copy) 8. │ ├─dplyr::same_src(x, y) 9. │ └─dplyr:::same_src.data.frame(x, y) 10. │ └─base::is.data.frame(y) 11. ├─... %>% suppressWarnings() 12. ├─base::suppressWarnings(.) 13. │ └─base::withCallingHandlers(...) 14. ├─dplyr::ungroup(.) 15. ├─dplyr::summarise(...) 16. ├─dplyr:::summarise.grouped_df(...) 17. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 18. │ └─base::withCallingHandlers(...) 19. ├─dplyr:::dplyr_internal_error(...) 20. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 21. │ └─rlang:::signal_abort(cnd, .file) 22. │ └─base::signalCondition(cnd) 23. └─dplyr (local) ``(``) 24. └─dplyr (local) handler(cnd) 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-ror.R:23:3'): estimate_ror_bygroup ───────────────────────────── Error in `summarise(., indi_pt_ps = sort(unique(indi_pt)), drugname_ps = paste(sort(unique(drugname)), collapse = " + "), start_dt_ps = unique(start_dt), .groups = "keep")`: i In argument: `indi_pt_ps = sort(unique(indi_pt))`. i In group 1: `primaryid = 100115733`, `caseid = 10011573`. Caused by error: ! `indi_pt_ps` must be size 1, not 0. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─faersquarterlydata::unify_tabular_ascii(ascii_list = faers_ascii_data) at test-ror.R:23:3 2. │ └─... %>% relocate(age_YR, .after = "age") 3. ├─dplyr::relocate(., age_YR, .after = "age") 4. ├─dplyr::mutate(...) 5. ├─dplyr::left_join(...) 6. ├─dplyr:::left_join.data.frame(...) 7. │ └─dplyr::auto_copy(x, y, copy = copy) 8. │ ├─dplyr::same_src(x, y) 9. │ └─dplyr:::same_src.data.frame(x, y) 10. │ └─base::is.data.frame(y) 11. ├─... %>% suppressWarnings() 12. ├─base::suppressWarnings(.) 13. │ └─base::withCallingHandlers(...) 14. ├─dplyr::ungroup(.) 15. ├─dplyr::summarise(...) 16. ├─dplyr:::summarise.grouped_df(...) 17. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 18. │ └─base::withCallingHandlers(...) 19. ├─dplyr:::dplyr_internal_error(...) 20. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 21. │ └─rlang:::signal_abort(cnd, .file) 22. │ └─base::signalCondition(cnd) 23. └─dplyr (local) ``(``) 24. └─dplyr (local) handler(cnd) 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-summary.R:4:3'): summary_faersdata ───────────────────────────── Error in `summarise(., indi_pt_ps = sort(unique(indi_pt)), drugname_ps = paste(sort(unique(drugname)), collapse = " + "), start_dt_ps = unique(start_dt), .groups = "keep")`: i In argument: `indi_pt_ps = sort(unique(indi_pt))`. i In group 1: `primaryid = 100115733`, `caseid = 10011573`. Caused by error: ! `indi_pt_ps` must be size 1, not 0. i To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─faersquarterlydata::unify_tabular_ascii(ascii_list = faers_ascii_data) at test-summary.R:4:3 2. │ └─... %>% relocate(age_YR, .after = "age") 3. ├─dplyr::relocate(., age_YR, .after = "age") 4. ├─dplyr::mutate(...) 5. ├─dplyr::left_join(...) 6. ├─dplyr:::left_join.data.frame(...) 7. │ └─dplyr::auto_copy(x, y, copy = copy) 8. │ ├─dplyr::same_src(x, y) 9. │ └─dplyr:::same_src.data.frame(x, y) 10. │ └─base::is.data.frame(y) 11. ├─... %>% suppressWarnings() 12. ├─base::suppressWarnings(.) 13. │ └─base::withCallingHandlers(...) 14. ├─dplyr::ungroup(.) 15. ├─dplyr::summarise(...) 16. ├─dplyr:::summarise.grouped_df(...) 17. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 18. │ └─base::withCallingHandlers(...) 19. ├─dplyr:::dplyr_internal_error(...) 20. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 21. │ └─rlang:::signal_abort(cnd, .file) 22. │ └─base::signalCondition(cnd) 23. └─dplyr (local) ``(``) 24. └─dplyr (local) handler(cnd) 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 3 | WARN 36 | SKIP 0 | PASS 37 ] Error: ! Test failures. Execution halted Package: FairMclus Check: whether package can be installed New result: ERROR Installation failed. Package: fbar Check: R code for possible problems New result: NOTE get_BiGG: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: filibustr Check: examples New result: ERROR Running examples in ‘filibustr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_hvw_data > ### Title: Get replication data from Harbridge-Yong, Volden, and Wiseman > ### (2023) > ### Aliases: get_hvw_data > > ### ** Examples > > ## Don't show: > if (!is.null(curl::nslookup("dataverse.harvard.edu", error = FALSE))) withAutoprint({ # examplesIf + ## End(Don't show) + get_hvw_data("senate") + ## Don't show: + }) # examplesIf > get_hvw_data("senate") Error in `httr2::req_perform()`: ! Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached [dvn-cloud.s3.amazonaws.com]: Connection timed out after 10001 milliseconds Backtrace: ▆ 1. ├─base::withAutoprint(...) 2. │ └─base::source(...) 3. │ ├─base::withVisible(eval(ei, envir)) 4. │ └─base::eval(ei, envir) 5. │ └─base::eval(ei, envir) 6. └─filibustr::get_hvw_data("senate") 7. └─filibustr:::get_online_data(url = url, source_name = "Harvard Dataverse") 8. └─httr2::req_perform(...) 9. └─httr2:::handle_resp(req, resp, error_call = error_call) 10. └─rlang::cnd_signal(resp) Execution halted Package: FLORAL Check: R code for possible problems New result: NOTE simu: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: forestmangr Check: examples New result: ERROR Running examples in ‘forestmangr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: huberwb > ### Title: Calculate the volume with bark of trees using the Huber method > ### Aliases: huberwb > > ### ** Examples > > library(forestmangr) > data("exfm8") > head(exfm8) # A tibble: 6 × 10 CLONE STRATA TREE LOG DBH TH hi di_wb bark_t sec_length 1 9318 4 1 1 17.6 21 0.5 18.5 6 1 2 9318 4 1 2 17.6 21 1.5 17.5 6 1 3 9318 4 1 3 17.6 21 2.5 17 5 1 4 9318 4 1 4 17.6 21 3.5 16.5 5 1 5 9318 4 1 5 17.6 21 4.5 16 4 1 6 9318 4 1 6 17.6 21 5.5 16 4 1 > > # Calculate the volume with bark using the Huber method: > huberwb(exfm8,"di_wb", "sec_length", "TREE") Error: ! The `add` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use the `.add` argument instead. Backtrace: ▆ 1. ├─forestmangr::huberwb(exfm8, "di_wb", "sec_length", "TREE") 2. │ └─... %>% dplyr::ungroup() 3. ├─dplyr::ungroup(.) 4. ├─dplyr::mutate(...) 5. ├─dplyr::group_by(., !!!.groups_syms, !!!tree_syms, add = T) 6. └─dplyr:::group_by.data.frame(...) 7. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 8. └─lifecycle::deprecate_stop("1.0.0", "group_by(add = )", "group_by(.add = )") 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) Execution halted Package: funModeling Check: examples New result: ERROR Running examples in ‘funModeling-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: categ_analysis > ### Title: Profiling analysis of categorical vs. target variable > ### Aliases: categ_analysis > > ### ** Examples > > categ_analysis(data_country, "country", "has_flu") Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. Backtrace: ▆ 1. ├─funModeling::categ_analysis(data_country, "country", "has_flu") 2. │ └─funModeling:::categ_analysis_logic(...) 3. │ └─... %>% arrange(-mean_target) 4. ├─dplyr::arrange(., -mean_target) 5. └─dplyr::summarise_(...) 6. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) Execution halted Package: funModeling Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘funModeling_quickstart.Rmd’ using rmarkdown Quitting from funModeling_quickstart.Rmd:222-224 [density_histogram] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. --- Backtrace: ▆ 1. ├─funModeling::plotar(...) 2. │ └─funModeling:::get_target_plot(data, input[i], target, plot_type) 3. │ └─funModeling:::histdens_target(data, input, target) 4. │ └─group_by_(data, target) %>% ... 5. └─dplyr::summarise_(., var.mean = interp(~mean(v, na.rm = T), v = as.name(input))) 6. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'funModeling_quickstart.Rmd' failed with diagnostics: `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. --- failed re-building ‘funModeling_quickstart.Rmd’ SUMMARY: processing the following file failed: ‘funModeling_quickstart.Rmd’ Error: Vignette re-building failed. Execution halted Package: gaiah Check: examples New result: ERROR Running examples in ‘gaiah-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: comboize_and_fortify > ### Title: prepare fortified output for multipanel plot > ### Aliases: comboize_and_fortify > > ### ** Examples > > # run through the example for comboize to get the variables > # mgen, miso, and mhab that we will use. > example(comboize) comboz> # first, run through the example for isotope_posterior_probs() to get comboz> # the rasters for two migrant birds. This gives us the list "birds2" comboz> example(isotope_posterior_probs) istp__> # obtain posterior probability rasters for the first 2 birds in the migrant_wiwa_isotopes istp__> # data set. This takes about 15 seconds on my laptop (most of that time is preparatory---once istp__> # that is done, each bird goes much faster). So we don't run it here. istp__> ## Not run: istp__> ##D birds2 <- isotope_posterior_probs(isoscape = isomap_job54152_prediction, istp__> ##D ref_birds = breeding_wiwa_isotopes, istp__> ##D assign_birds = migrant_wiwa_isotopes[1:2,] istp__> ##D ) istp__> ## End(Not run) istp__> istp__> # However, you can load the results as a saved data object to see what they look like: istp__> birds2 <- example_isotope_posteriors istp__> # Since the ref_birds above were separate from the migrant birds, no leave-one-out was istp__> # performed. Hence birds2$loo_results is NULL, and all the results are in istp__> # birds2$regular. istp__> istp__> # Look at the names of the resulting output for the first bird: istp__> names(birds2$regular[[1]]) [1] "posterior_probs" "assignment_parameters" istp__> names(birds2$regular[[1]]$assignment_parameters) [1] "Tilde_T_mu" "R_sigma_squared" "a_bar" "b_bar" [5] "sd_indiv" istp__> # If you want to do self-assignment for a whole bunch of reference birds, it takes much longer. istp__> # It looks like this: istp__> ## Not run: istp__> ##D self_ass <- isotope_posterior_probs(isoscape = isomap_job54152_prediction, istp__> ##D ref_birds = breeding_wiwa_isotopes, istp__> ##D self_assign = TRUE) istp__> ## End(Not run) istp__> istp__> istp__> comboz> # extract the posterior probs rasters from that output into a raster stack comboz> miso <- lapply(birds2$regular, function(x) x$posterior_probs) %>% comboz+ raster::stack() comboz> # see the names of the birds we are dealing with: comboz> names(miso) [1] "WIWA02" "WIWA03" comboz> # get the genetic posteriors for those two birds comboz> mig_gen2 <- migrant_wiwa_genetic_posteriors %>% comboz+ dplyr::filter(ID %in% c(names(miso))) comboz> # make genetic posterior rasters for those two birds, make sure they are comboz> # sorted in the same order as miso, and make a raster stack of it comboz> mgen <- genetic_posteriors2rasters(G = mig_gen2, R = genetic_regions)[names(miso)] %>% comboz+ raster::stack() comboz> # make a normalized prior from habitat quality that is zeros everywhere comboz> # outside of the "known" range. comboz> tmp <- wiwa_habitat_unclipped * wiwa_breed comboz> mhab <- tmp / raster::cellStats(tmp, sum) comboz> # combine genetics, isotopes and habitat with exponents of 1 on each comboz> mcombo <- comboize(mgen, miso, mhab, 1, 1, 1) > > # then run that on the first bird to get a data frame > # that you can use with ggplot > ff <- comboize_and_fortify(mgen[[1]], miso[[1]], mhab) Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. ├─gaiah::comboize_and_fortify(mgen[[1]], miso[[1]], mhab) 2. │ ├─... %>% dplyr::bind_rows(.id = "genetics_beta") 3. │ └─base::lapply(...) 4. │ └─gaiah (local) FUN(X[[i]], ...) 5. │ ├─... %>% dplyr::bind_rows(.id = "isotope_beta") 6. │ └─base::lapply(...) 7. │ └─gaiah (local) FUN(X[[i]], ...) 8. │ ├─... %>% dplyr::bind_rows(.id = "habitat_beta") 9. │ └─base::lapply(...) 10. │ └─gaiah (local) FUN(X[[i]], ...) 11. │ └─... %>% dplyr::tbl_df() 12. ├─dplyr::bind_rows(., .id = "genetics_beta") 13. │ └─rlang::list2(...) 14. ├─dplyr::bind_rows(., .id = "isotope_beta") 15. │ └─rlang::list2(...) 16. ├─dplyr::bind_rows(., .id = "habitat_beta") 17. │ └─rlang::list2(...) 18. └─dplyr::tbl_df(.) 19. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 20. └─lifecycle:::deprecate_stop0(msg) 21. └─rlang::cnd_signal(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed comboize 8.08 0.302 8.388 Package: gap Check: R code for possible problems New result: NOTE qtl2dplotly: no visible binding for global variable ‘id’ qtl3dplotly: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: gapclosing Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gapclosing.Rmd’ using rmarkdown Quitting from gapclosing.Rmd:113-115 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarize()`: ℹ In argument: `x = ifelse(gapclosing.category == category_A, 0.8, 2.2)`. ℹ In group 1: `gapclosing.category = A`. Caused by error: ! `x` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─base::plot(estimate, return_plots = TRUE) 2. ├─gapclosing:::plot.gapclosing(estimate, return_plots = TRUE) 3. │ └─base::lapply(...) 4. │ └─gapclosing (local) FUN(X[[i]], ...) 5. │ └─gapclosing::disparityplot(...) 6. │ ├─ggplot2::geom_text(...) 7. │ │ └─ggplot2::layer(...) 8. │ │ └─ggplot2::fortify(data) 9. │ └─means %>% dplyr::group_by(gapclosing.category) %>% ... 10. ├─dplyr::summarize(...) 11. ├─dplyr:::summarise.grouped_df(...) 12. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 13. │ └─base::withCallingHandlers(...) 14. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'gapclosing.Rmd' failed with diagnostics: ℹ In argument: `x = ifelse(gapclosing.category == category_A, 0.8, 2.2)`. ℹ In group 1: `gapclosing.category = A`. Caused by error: ! `x` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘gapclosing.Rmd’ SUMMARY: processing the following file failed: ‘gapclosing.Rmd’ Error: Vignette re-building failed. Execution halted Package: genogeographer Check: examples New result: ERROR Running examples in ‘genogeographer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: LR_table > ### Title: Compute pairwise likelihood ratios > ### Aliases: LR_table > > ### ** Examples > > df_ <- simulate_pops(pop_n = 4, aims_n = 50) > df_db <- pops_to_DB(df_) Error: ! `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─genogeographer::pops_to_DB(df_) 2. │ └─genogeographer:::score_add_df(db, ...) 3. │ └─db %>% ... 4. └─dplyr::select_(...) 5. └─dplyr:::lazy_defunct("select", hint = FALSE) 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: GerminaR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘GerminaQuant.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. [WARNING] Citeproc: citation R-GerminaR not found --- finished re-building ‘GerminaQuant.Rmd’ --- re-building ‘GerminaR.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘GerminaR.Rmd’ --- re-building ‘introduction.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://www.zotero.org/styles/apa HttpExceptionRequest Request { host = "www.zotero.org" port = 443 secure = True requestHeaders = [] path = "/styles/apa" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } ResponseTimeout Error: processing vignette 'introduction.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘introduction.Rmd’ SUMMARY: processing the following file failed: ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: GFE Check: examples New result: ERROR Running examples in ‘GFE-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: reSamGF > ### Title: Gross flows variance estimation. > ### Aliases: reSamGF > > ### ** Examples > > library(TeachingSampling) Loading required package: dplyr Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: magrittr > library(data.table) Attaching package: ‘data.table’ The following objects are masked from ‘package:dplyr’: between, first, last The following object is masked from ‘package:base’: %notin% > # Colombia's electoral candidates in 2014 > candidates_t0 <- c("Clara","Enrique","Santos","Martha","Zuluaga","Blanco", "NoVoto") > candidates_t1 <- c("Santos","Zuluaga","Blanco", "NoVoto") > > N <- 100000 > nCanT0 <- length(candidates_t0) > nCanT1 <- length(candidates_t1) > > # Initial probabilities > eta <- matrix(c(0.10, 0.10, 0.20, 0.17, 0.28, 0.1, 0.05), + byrow = TRUE, nrow = nCanT0) > # Transition probabilities > P <- matrix(c(0.10, 0.60, 0.15, 0.15, + 0.30, 0.10, 0.25, 0.35, + 0.34, 0.25, 0.16, 0.25, + 0.25, 0.05, 0.35, 0.35, + 0.10, 0.25, 0.45, 0.20, + 0.12, 0.36, 0.22, 0.30, + 0.10, 0.15, 0.30, 0.45), + byrow = TRUE, nrow = nCanT0) > > citaMod <- matrix(, ncol = nCanT1, nrow = nCanT0) > row.names(citaMod) <- candidates_t0 > colnames(citaMod) <- candidates_t1 > > for(ii in 1:nCanT0){ + citaMod[ii,] <- c(rmultinom(1, size = N * eta[ii,], prob = P[ii,])) + } > > # # Model I > psiI <- 0.9 > rhoRRI <- 0.9 > rhoMMI <- 0.5 > > citaModI <- matrix(nrow = nCanT0 + 1, ncol = nCanT1 + 1) > rownames(citaModI) <- c(candidates_t0, "Non_Resp") > colnames(citaModI) <- c(candidates_t1, "Non_Resp") > > citaModI[1:nCanT0, 1:nCanT1] <- P * c(eta) * rhoRRI * psiI > citaModI[(nCanT0 + 1), (nCanT1 + 1)] <- rhoMMI * (1-psiI) > citaModI[1:nCanT0, (nCanT1 + 1)] <- (1-rhoRRI) * psiI * rowSums(P * c(eta)) > citaModI[(nCanT0 + 1), 1:nCanT1 ] <- (1-rhoMMI) * (1-psiI) * colSums(P * c(eta)) > citaModI <- round_preserve_sum(citaModI * N) > DBcitaModI <- createBase(citaModI) > > # Creating auxiliary information > DBcitaModI[,AuxVar := rnorm(nrow(DBcitaModI), mean = 45, sd = 10)] > # Selects a sample with unequal probabilities > res <- S.piPS(n = 1200, as.data.frame(DBcitaModI)[,"AuxVar"]) > sam <- res[,1] > pik <- res[,2] > DBcitaModISam <- copy(DBcitaModI[sam,]) > DBcitaModISam[,Pik := pik] > > # Gross flows estimation > estima <- estGF(sampleBase = DBcitaModISam, niter = 500, model = "II", colWeights = "Pik") > # gross flows variance estimation > varEstima <- reSamGF(sampleBase = DBcitaModISam, type = "Bootstrap", nRepBoot = 100, + model = "II", niter = 101, colWeights = "Pik") Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─GFE::reSamGF(...) 2. │ └─GFE (local) varParam(EstGF) 3. │ └─... %>% as.data.frame() 4. ├─base::as.data.frame(.) 5. ├─dplyr::summarize_all(...) 6. │ └─dplyr:::manip_all(...) 7. │ ├─rlang::syms(tbl_nongroup_vars(.tbl)) 8. │ │ └─rlang:::map(x, sym) 9. │ │ └─base::lapply(.x, .f, ...) 10. │ └─dplyr::tbl_nongroup_vars(.tbl) 11. │ ├─generics::setdiff(tbl_vars(x), group_vars(x)) 12. │ └─dplyr::tbl_vars(x) 13. │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x)) 14. │ │ └─base::structure(...) 15. │ └─dplyr:::tbl_vars_dispatch(x) 16. └─dplyr::group_by_(., var2) 17. └─dplyr:::lazy_defunct("group_by") 18. └─lifecycle::deprecate_stop(...) 19. └─lifecycle:::deprecate_stop0(msg) 20. └─rlang::cnd_signal(...) Execution halted Package: ggalluvial Check: dependencies in R code New result: WARNING Missing or unexported object: ‘dplyr::select_vars’ Package: ggbrick Check: R code for possible problems New result: NOTE robust_random: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: ggFishPlots Check: R code for possible problems New result: NOTE plot_growth: no visible binding for global variable ‘id’ plot_lw: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: gggenomes Check: R code for possible problems New result: NOTE makeContent.genetree: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: gglm Check: R code for possible problems New result: NOTE fortify.mlogit: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: ggmulti Check: R code for possible problems New result: NOTE collide_ : : no visible binding for global variable ‘location’ compute_scales.histogram: no visible binding for global variable ‘location’ Undefined global functions or variables: location Package: ghypernet Check: R code for possible problems New result: NOTE .bccm: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: gitgadget Check: R code for possible problems New result: NOTE fetch_work: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: glyrepr Check: tests New result: ERROR Running ‘testthat.R’ [38s/39s] 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(glyrepr) > > test_check("glyrepr") Saving _problems/test-composition-261.R [ FAIL 1 | WARN 43 | SKIP 10 | PASS 1139 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (10): 'test-composition.R:268:1', 'test-example-glycans.R:1:1', 'test-example-glycans.R:9:1', 'test-example-glycans.R:16:1', 'test-example-glycans.R:23:1', 'test-example-glycans.R:30:1', 'test-structure-level.R:61:1', 'test-structure.R:500:1', 'test-structure.R:507:1', 'test-structure.R:515:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-composition.R:261:3'): large composition printing performance is acceptable ── Expected `as.numeric(end_time - start_time) < 1` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 43 | SKIP 10 | PASS 1139 ] Error: ! Test failures. Execution halted Package: gmgm Check: R code for possible problems New result: NOTE network: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: gMOIP Check: R code for possible problems New result: NOTE addNDSet: no visible binding for global variable ‘id’ classifyNDSet: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: goat Check: R code for possible problems New result: NOTE build_treemap: no visible binding for global variable ‘id’ go_gene2go: no visible binding for global variable ‘id’ load_genesets_gmtfile: no visible binding for global variable ‘id’ load_genesets_go_bioconductor: no visible binding for global variable ‘id’ load_genesets_go_fromfile: no visible binding for global variable ‘id’ load_genesets_syngo: no visible binding for global variable ‘id’ ontology_data_structures: no visible binding for global variable ‘id’ plot_lollipop: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: googletraffic Check: R code for possible problems New result: NOTE gt_make_grid: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: GOxploreR Check: whether package can be installed New result: ERROR Installation failed. Package: gratis Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘QuickStart.Rmd’ using rmarkdown Quitting from QuickStart.Rmd:106-121 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `summarise()`: ℹ In argument: `value = my_features(value)`. ℹ In group 1: `key = "Series 1"`. Caused by error: ! `value` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─df %>% as_tibble() %>% group_by(key) %>% ... 2. ├─dplyr::summarise(...) 3. ├─dplyr:::summarise.grouped_df(...) 4. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 5. │ └─base::withCallingHandlers(...) 6. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'QuickStart.Rmd' failed with diagnostics: ℹ In argument: `value = my_features(value)`. ℹ In group 1: `key = "Series 1"`. Caused by error: ! `value` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘QuickStart.Rmd’ SUMMARY: processing the following file failed: ‘QuickStart.Rmd’ Error: Vignette re-building failed. Execution halted Package: growthcleanr Check: R code for possible problems New result: NOTE cleanadult: no visible binding for global variable ‘id’ cleangrowth: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: grPipe Check: R code for possible problems New result: NOTE grPipe.plot: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: halk Check: examples New result: ERROR Running examples in ‘halk-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: calc_stat_scores > ### Title: Compute test statistics for comparing actual and estimated ages > ### Aliases: calc_stat_scores calc_ks_score calc_chi_score > > ### ** Examples > > halk <- make_halk(spp_data, levels = c("spp")) > newdat <- laa_data > newdat$spp <- "bluegill" > pred_ages <- assign_ages(newdat, halk) > calc_ks_score(pred_ages) Error in `dplyr::summarize()`: ℹ In argument: `ks.stat = purrr::map_df(...)`. ℹ In group 1: `spp = "bluegill"`. Caused by error: ! `ks.stat` must be size 1, not 11. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─halk::calc_ks_score(pred_ages) 2. │ └─... %>% dplyr::ungroup() 3. ├─dplyr::ungroup(.) 4. ├─tidyr::unnest(., cols = c(.data$ks.stat)) 5. ├─dplyr::summarize(...) 6. ├─dplyr:::summarise.grouped_df(...) 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) ``(``) 14. └─dplyr (local) handler(cnd) 15. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: HVT Check: R code for possible problems New result: NOTE getCellId: no visible binding for global variable ‘id’ plotHVT: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: IAT Check: examples New result: ERROR Running examples in ‘IAT-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cleanIAT > ### Title: Clean IAT data using the updated D-Scoring algorithm > ### Aliases: cleanIAT > > ### ** Examples > > # Get Ps who recieve Math-Male sorting task in first blocks > > cong_first <- IATData[IATData$isCongruentFirst == 1, ] > > dscore_first <- cleanIAT(my_data = cong_first, + block_name = "BLOCK_NAME_S", + trial_blocks = c("BLOCK2", "BLOCK3", "BLOCK5", "BLOCK6"), + session_id = "SESSION_ID", + trial_latency = "TRIAL_LATENCY", + trial_error = "TRIAL_ERROR", + v_error = 1, v_extreme = 2, v_std = 1) Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─IAT::cleanIAT(...) 2. │ └─... %>% ... 3. └─dplyr::filter_(., interp(~x < 10000 & x >= 0, x = as.name(trial_latency))) 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: immunarch Check: examples New result: ERROR Running examples in ‘immunarch-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: airr_public > ### Title: Public indices - pairwise repertoire overlap > ### Aliases: airr_public airr_public_intersection airr_public_jaccard > > ### ** Examples > > # Limit the number of threads used by the underlying DB for this session. > # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers). > db_exec("SET threads TO 1") > # Load data > immdata <- get_test_idata() |> agg_repertoires("Therapy") Rows: 2 Columns: 4 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (4): File, Therapy, Response, Prefix 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. ℹ Found 2/2 repertoire files from the metadata on the disk ✔ Metadata parsed successfully ── Reading repertoire data 1. /home/hornik/tmp/CRAN_recheck/Library/immundata/extdata/tsv/sample_0_1k.tsv 2. /home/hornik/tmp/CRAN_recheck/Library/immundata/extdata/tsv/sample_1k_2k.tsv ℹ Checking if all files are of the same type ✔ All files have the same extension ── Renaming the columns and schemas ✔ Renaming is finished ── Preprocessing the data 1. exclude_columns 2. filter_nonproductive ✔ Preprocessing plan is ready ── Aggregating the data to receptors ℹ No locus information found ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible ✔ Execution plan for receptor data aggregation and annotation is ready ── Joining the metadata table with the dataset using 'filename' column ✔ Joining plan is ready ── Postprocessing the data 1. prefix_barcodes ✔ Postprocessing plan is ready ── Saving the newly created ImmunData to disk ℹ Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpfeHF7h/file37996512ffe398/annotations.parquet] ℹ Writing the metadata to [/home/hornik/tmp/scratch/RtmpfeHF7h/file37996512ffe398/metadata.json] ✔ ImmunData files saved to [/home/hornik/tmp/scratch/RtmpfeHF7h/file37996512ffe398] ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpfeHF7h/file37996512ffe398'] ✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpfeHF7h/file37996512ffe398'] ── Summary ℹ Time elapsed: 4.18 secs Error in `count()`: ! This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. ℹ See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure Backtrace: ▆ 1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy") 2. │ └─checkmate::assert_r6(idata, "ImmunData") 3. │ └─checkmate::checkR6(...) 4. ├─immundata::get_test_idata() 5. │ └─immundata:::get_test_idata_tsv_with_metadata() 6. │ └─immundata::read_repertoires(...) 7. │ ├─dplyr::pull(count(idata), "n") 8. │ ├─dplyr::count(idata) 9. │ └─immundata:::count.ImmunData(idata) 10. │ ├─dplyr::count(x$annotations) 11. │ └─duckplyr:::count.duckplyr_df(x$annotations) 12. │ ├─duckplyr:::rel_try(...) 13. │ │ └─rlang::try_fetch(rel, error = identity) 14. │ │ ├─base::tryCatch(...) 15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 18. │ │ └─base::withCallingHandlers(...) 19. │ └─dplyr:::tally_n(...) 20. │ └─rlang::quo_is_null(wt) 21. └─rlang::abort(message = message) Execution halted Package: immundata Check: tests New result: ERROR Running ‘testthat.R’ [71s/45s] 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(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.5 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b17e88898/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b17e88898/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b17e88898] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b17e88898'] > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b17e88898'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 3.83 secs Saving _problems/test-annotate-barcodes-2.R > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b678678c872a/annotations.parquet] > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b678678c872a/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b678678c872a] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b678678c872a'] > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b678678c872a'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 4.8 secs Saving _problems/test-annotate-receptors-2.R > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b30918449/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b30918449/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b30918449] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b30918449'] > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b30918449'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 3.49 secs Saving _problems/test-filter-barcodes-4.R > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67844dc64b9/annotations.parquet] > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67844dc64b9/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67844dc64b9] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67844dc64b9'] > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67844dc64b9'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 3.2 secs Saving _problems/test-filter-immundata-exact-2.R > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b423b77cf/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b423b77cf/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b423b77cf] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b423b77cf'] > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b423b77cf'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.58 secs > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b6783ca4cd6a/annotations.parquet] Saving _problems/test-filter-immundata-hamm-3.R > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b6783ca4cd6a/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b6783ca4cd6a] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b6783ca4cd6a'] > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b6783ca4cd6a'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.31 secs > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b2f14b9a4/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67871b5664a/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b2f14b9a4/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b2f14b9a4] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b2f14b9a4'] > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b2f14b9a4'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 3.44 secs > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67871b5664a/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67871b5664a] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67871b5664a'] > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67871b5664a'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 2.92 secs Saving _problems/test-filter-immundata-regex-2.R > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix Saving _problems/test-filter-immundata-lev-3.R Saving _problems/test-filter-immundata-lev-29.R > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-immundata.R: 2. filter_nonproductive > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67846a98b93/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67846a98b93/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67846a98b93] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67846a98b93'] > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/file22b67846a98b93'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 3.56 secs > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes Saving _problems/test-filter-receptors-3.R > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b26bdbfe0/annotations.parquet] > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Respons > test-io-repertoires.R: e, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: 2. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b26bdbfe0/metadata.json] > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b26bdbfe0] > test-io-repertoires.R: 1. exclude_columns > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b26bdbfe0'] > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b26bdbfe0'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.6 secs > test-io-repertoires.R: 2. filter_nonproductive > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b3be02cc0/annotations.parquet] > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b3be02cc0/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp76fion/file22b67b3be02cc0] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b3be02cc0'] > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp76fion/file22b67b3be02cc0'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-io-repertoires.R: v Postprocessing plan is ready > test-filter-immundata.R: i Time elapsed: 3.9 secs > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/annotations.parquet] Saving _problems/test-filter-immundata-2.R Saving _problems/test-filter-immundata-20.R > test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 5.07 secs > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: 2. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 4.21 secs > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-no-barcodes/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-no-barcodes/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-no-barcodes] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-no-barcodes'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-no-barcodes'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.91 secs > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.89 secs > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: v_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-rename/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-rename/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-rename] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-rename'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-rename'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.66 secs > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: j_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude-rename/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude-rename/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude-rename] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude-rename'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp2VJFtV/test-exclude-rename'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.56 secs > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/CRAN_recheck/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors Saving _problems/test-io-repertoires-28.R Saving _problems/test-io-repertoires-56.R Saving _problems/test-io-repertoires-83.R Saving _problems/test-io-repertoires-120.R Saving _problems/test-io-repertoires-146.R Saving _problems/test-io-repertoires-176.R [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure ── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ── Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame. i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr. i See `vignette("prudence")` for other options. Caused by error in `quo_is_null()`: ! `quo` must be a quosure [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ] Error: ! Test failures. Execution halted Package: inspectdf Check: examples New result: ERROR Running examples in ‘inspectdf-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: show_plot > ### Title: Simple graphical inspection of dataframe summaries > ### Aliases: show_plot > > ### ** Examples > > # Load 'starwars' data > data("starwars", package = "dplyr") > > # Horizontal bar plot for categorical column composition > x <- inspect_cat(starwars) > show_plot(x) Error in `group_by()`: ! Must group by variables found in `.data`. ✖ Column `col_name` is not found. Backtrace: ▆ 1. ├─inspectdf::show_plot(x) 2. │ └─inspectdf:::plot_cat(x, ...) 3. │ └─inspectdf:::collapse_levels(lvl_df, i) 4. │ └─... %>% mutate(level_key = paste0(value, "-", col_name)) 5. ├─dplyr::mutate(., level_key = paste0(value, "-", col_name)) 6. ├─dplyr::arrange(., col_name) 7. ├─dplyr::ungroup(.) 8. ├─dplyr::mutate(., colvalstretch = colvalstretch * (1 - 0.8 * (1/length(colval)))) 9. ├─dplyr::mutate(...) 10. ├─dplyr::mutate(., colval = cumsum(prop)) 11. ├─dplyr::group_by(., col_name) 12. └─dplyr:::group_by.data.frame(., col_name) 13. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 14. └─rlang::abort(bullets, call = error_call) Execution halted Package: ipft Check: examples New result: ERROR Running examples in ‘ipft-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ipfGroup > ### Title: Creates groups based on the specified parameters > ### Aliases: ipfGroup > > ### ** Examples > > > group <- ipfGroup(mtcars, cyl) Error: ! The `...` argument of `group_indices()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please `group_by()` first Backtrace: ▆ 1. └─ipft::ipfGroup(mtcars, cyl) 2. ├─dplyr::group_indices(data, ...) 3. └─dplyr:::group_indices.data.frame(data, ...) 4. └─lifecycle::deprecate_stop("1.0.0", "group_indices(... = )", details = "Please `group_by()` first") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed ipfDistance 4.715 0.104 5.043 Package: ir Check: examples New result: ERROR Running examples in ‘ir-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: summarize > ### Title: Summarize each group in a 'ir' object to fewer rows > ### Aliases: summarize summarize.ir summarise summarise.ir > > ### ** Examples > > ## summarize > > # select in each sample_type groups the first spectrum > ir_sample_data |> + dplyr::group_by(sample_type) |> + dplyr::summarize(spectra = spectra[[1]]) Error in `ir_reclass_ir()`: ℹ In argument: `spectra = spectra[[1]]`. ℹ In group 1: `sample_type = "hardwood"`. Caused by error: ! `spectra` must be size 1, not 3351. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─dplyr::summarize(...) 2. ├─ir:::summarise.ir(...) 3. │ └─ir:::ir_reclass_ir(NextMethod()) 4. ├─base::NextMethod() 5. ├─dplyr:::summarise.grouped_df(dplyr::group_by(ir_sample_data, sample_type), spectra = spectra[[1]]) 6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 7. │ └─base::withCallingHandlers(...) 8. ├─dplyr:::dplyr_internal_error(...) 9. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 10. │ └─rlang:::signal_abort(cnd, .file) 11. │ └─base::signalCondition(cnd) 12. └─dplyr (local) ``(``) 13. └─dplyr (local) handler(cnd) 14. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: IVPP Check: package dependencies New result: ERROR Package required but not available: ‘bootnet’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: khisr Check: R code for possible problems New result: NOTE get_data_elements_with_category_options: no visible binding for global variable ‘id’ get_data_sets_by_level: no visible binding for global variable ‘id’ get_organisations_by_level: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: kollaR Check: R code for possible problems New result: NOTE static_plot: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: LAGOSNE Check: tests New result: ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(LAGOSNE) > > test_check("LAGOSNE") Saving _problems/test-lake_info-8.R Saving _problems/test-lake_info-41.R [ FAIL 2 | WARN 0 | SKIP 11 | PASS 3 ] ══ Skipped tests (11) ══════════════════════════════════════════════════════════ • On CRAN (11): 'test-info_table.R:4:3', 'test-lagos_get.R:5:3', 'test-lagos_get.R:15:3', 'test-lagos_load.R:5:3', 'test-lagos_load.R:17:3', 'test-lagos_load.R:28:3', 'test-lagos_select.R:5:3', 'test-lagos_select.R:101:3', 'test-lake_info.R:17:3', 'test-lake_info.R:27:3', 'test_display-names.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lake_info.R:7:3'): lake_info works ───────────────────────────── Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-lake_info.R:7:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(lake_info(name = "Pine Lake", state = "Iowa", dt = dt)) 5. └─LAGOSNE::lake_info(name = "Pine Lake", state = "Iowa", dt = dt) 6. ├─base::do.call(...) 7. └─base::apply(...) 8. └─LAGOSNE (local) FUN(newX[, i], ...) 9. └─LAGOSNE:::lake_info_(...) 10. └─dplyr::filter_(dt_filter, filter_criteria) 11. └─dplyr:::lazy_defunct("filter") 12. └─lifecycle::deprecate_stop(...) 13. └─lifecycle:::deprecate_stop0(msg) 14. └─rlang::cnd_signal(...) ── Failure ('test-lake_info.R:40:3'): lake_info fails well ───────────────────── `lake_info(name = "gibberish", state = "Wisconsin", dt = dt)` threw an error with unexpected message. Expected match: "Lake 'gibberish' in Wisconsin not found" Actual message: "`filter_()` was deprecated in dplyr 0.7.0 and is now defunct.\nℹ Please use `filter()` instead.\nℹ See vignette('programming') for more help" Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-lake_info.R:40:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─LAGOSNE::lake_info(name = "gibberish", state = "Wisconsin", dt = dt) 7. ├─base::do.call(...) 8. └─base::apply(...) 9. └─LAGOSNE (local) FUN(newX[, i], ...) 10. └─LAGOSNE:::lake_info_(...) 11. └─dplyr::filter_(dt_filter, filter_criteria) 12. └─dplyr:::lazy_defunct("filter") 13. └─lifecycle::deprecate_stop(...) 14. └─lifecycle:::deprecate_stop0(msg) 15. └─rlang::cnd_signal(...) [ FAIL 2 | WARN 0 | SKIP 11 | PASS 3 ] Error: ! Test failures. Execution halted Package: Lahman Check: examples New result: ERROR Running examples in ‘Lahman-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Fielding > ### Title: Fielding table > ### Aliases: Fielding > ### Keywords: datasets > > ### ** Examples > > data(Fielding) > # Basic fielding data > > require("dplyr") Loading required package: dplyr Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > > > # Roberto Clemente's fielding profile > # pitching and catching related data removed > # subset(Fielding, playerID == "clemero01")[, 1:13] > Fielding %>% + filter(playerID == "clemero01") %>% + select(1:13) playerID yearID stint teamID lgID POS G GS InnOuts PO A E DP 1 clemero01 1955 1 PIT NL OF 118 107 2892 253 18 6 5 2 clemero01 1956 1 PIT NL 2B 2 0 18 1 1 1 0 3 clemero01 1956 1 PIT NL 3B 1 0 6 0 2 1 0 4 clemero01 1956 1 PIT NL OF 139 130 3499 274 17 13 2 5 clemero01 1957 1 PIT NL OF 109 107 2836 272 9 6 1 6 clemero01 1958 1 PIT NL OF 135 129 3452 312 22 6 3 7 clemero01 1959 1 PIT NL OF 104 102 2700 229 10 13 1 8 clemero01 1960 1 PIT NL OF 142 140 3767 246 19 8 2 9 clemero01 1961 1 PIT NL OF 144 142 3723 256 27 9 5 10 clemero01 1962 1 PIT NL OF 142 138 3686 269 19 8 1 11 clemero01 1963 1 PIT NL OF 151 148 3943 239 11 11 2 12 clemero01 1964 1 PIT NL OF 154 154 4085 289 13 10 2 13 clemero01 1965 1 PIT NL OF 145 143 3810 288 16 10 1 14 clemero01 1966 1 PIT NL OF 154 153 4147 318 17 12 3 15 clemero01 1967 1 PIT NL OF 145 141 3751 273 17 9 4 16 clemero01 1968 1 PIT NL OF 131 128 3477 297 9 5 1 17 clemero01 1969 1 PIT NL OF 135 128 3372 226 14 5 1 18 clemero01 1970 1 PIT NL OF 104 102 2703 189 12 7 2 19 clemero01 1971 1 PIT NL OF 124 120 3243 267 11 2 4 20 clemero01 1972 1 PIT NL OF 94 88 2436 199 5 0 2 > > # Yadier Molina's fielding profile > # PB, WP, SP and CS apply to catchers > Fielding %>% + subset(playerID == "molinya01") %>% + select(-WP, -ZR) playerID yearID stint teamID lgID POS G GS InnOuts PO A E DP PB 95162 molinya01 2004 1 SLN NL C 51 39 1032 256 16 2 1 4 95163 molinya01 2005 1 SLN NL C 114 111 2878 684 66 7 4 8 95164 molinya01 2005 1 SLN NL 1B 1 0 3 0 0 0 0 NA 95165 molinya01 2006 1 SLN NL C 127 118 3112 734 79 4 6 7 95166 molinya01 2006 1 SLN NL 1B 4 0 15 5 0 1 1 NA 95167 molinya01 2007 1 SLN NL C 107 101 2584 582 63 6 8 7 95168 molinya01 2007 1 SLN NL 1B 1 0 3 1 0 0 0 NA 95169 molinya01 2008 1 SLN NL C 119 114 3006 653 70 10 7 5 95170 molinya01 2008 1 SLN NL 1B 2 1 33 13 3 0 1 NA 95171 molinya01 2009 1 SLN NL C 138 136 3530 884 82 5 6 4 95172 molinya01 2009 1 SLN NL 1B 6 0 30 10 1 0 2 NA 95173 molinya01 2010 1 SLN NL C 135 130 3414 895 79 5 10 7 95174 molinya01 2010 1 SLN NL 1B 7 0 21 7 0 0 2 NA 95175 molinya01 2011 1 SLN NL C 137 132 3450 857 67 5 5 6 95176 molinya01 2011 1 SLN NL 1B 2 0 6 3 0 1 0 NA 95177 molinya01 2012 1 SLN NL C 136 133 3484 962 88 3 12 6 95178 molinya01 2012 1 SLN NL 1B 3 0 27 11 2 0 0 NA 95179 molinya01 2013 1 SLN NL C 131 129 3346 976 63 4 11 3 95180 molinya01 2013 1 SLN NL 1B 5 2 54 17 1 0 1 NA 95181 molinya01 2014 1 SLN NL C 107 106 2795 810 56 2 10 3 95182 molinya01 2014 1 SLN NL 1B 1 1 27 10 1 0 0 NA 95183 molinya01 2015 1 SLN NL C 134 131 3449 1064 56 7 9 4 95184 molinya01 2016 1 SLN NL C 146 142 3655 1113 60 2 5 8 95185 molinya01 2016 1 SLN NL 1B 2 1 21 10 1 0 0 NA 95186 molinya01 2017 1 SLN NL C 133 133 3377 1082 55 7 13 6 95187 molinya01 2017 1 SLN NL 1B 1 0 6 4 0 0 0 NA 95188 molinya01 2018 1 SLN NL C 121 120 3053 966 42 2 8 4 95189 molinya01 2018 1 SLN NL 1B 5 0 36 9 2 1 3 NA 95190 molinya01 2019 1 SLN NL C 111 108 2818 916 30 1 5 4 95191 molinya01 2019 1 SLN NL 1B 4 0 24 6 0 0 1 NA 95192 molinya01 2019 1 SLN NL 3B 1 0 3 0 0 0 0 NA 95193 molinya01 2020 1 SLN NL C 42 42 1012 307 16 5 1 3 95194 molinya01 2020 1 SLN NL 1B 2 0 15 3 0 0 0 NA 95195 molinya01 2021 1 SLN NL C 118 118 3004 869 49 3 10 6 95196 molinya01 2021 1 SLN NL 1B 1 0 9 1 1 0 0 NA 95197 molinya01 2022 1 SLN NL P 2 0 6 0 0 0 0 NA 95198 molinya01 2022 1 SLN NL C 77 71 1885 512 25 3 6 1 95199 molinya01 2022 1 SLN NL 1B 1 0 3 0 0 0 0 NA SB CS 95162 9 8 95163 14 25 95164 NA NA 95165 37 29 95166 NA NA 95167 23 27 95168 NA NA 95169 34 18 95170 NA NA 95171 32 22 95172 NA NA 95173 35 33 95174 NA NA 95175 46 19 95176 NA NA 95177 38 35 95178 NA NA 95179 26 20 95180 NA NA 95181 23 21 95182 NA NA 95183 37 26 95184 67 18 95185 NA NA 95186 43 24 95187 NA NA 95188 27 12 95189 NA NA 95190 22 8 95191 NA NA 95192 NA NA 95193 6 5 95194 NA NA 95195 26 18 95196 NA NA 95197 NA NA 95198 20 13 95199 NA NA > > # Pedro Martinez's fielding profile > Fielding %>% subset(playerID == "martipe02") playerID yearID stint teamID lgID POS G GS InnOuts PO A E DP PB WP SB 86668 martipe02 1992 1 LAN NL P 2 1 24 0 0 0 0 NA NA NA 86669 martipe02 1993 1 LAN NL P 65 2 321 4 4 0 1 NA NA NA 86670 martipe02 1994 1 MON NL P 24 23 434 9 15 4 0 NA NA NA 86671 martipe02 1995 1 MON NL P 30 30 584 14 23 2 0 NA NA NA 86672 martipe02 1996 1 MON NL P 33 33 650 11 17 3 1 NA NA NA 86673 martipe02 1997 1 MON NL P 31 31 724 7 31 1 1 NA NA NA 86674 martipe02 1998 1 BOS AL P 33 33 701 11 18 4 3 NA NA NA 86675 martipe02 1999 1 BOS AL P 31 29 640 13 15 1 0 NA NA NA 86676 martipe02 2000 1 BOS AL P 29 29 651 14 28 0 2 NA NA NA 86677 martipe02 2001 1 BOS AL P 18 18 350 5 5 0 0 NA NA NA 86678 martipe02 2002 1 BOS AL P 30 30 598 16 16 2 1 NA NA NA 86679 martipe02 2003 1 BOS AL P 29 29 560 14 20 0 0 NA NA NA 86680 martipe02 2004 1 BOS AL P 33 33 651 16 16 1 0 NA NA NA 86681 martipe02 2005 1 NYN NL P 31 31 651 6 19 0 0 NA NA NA 86682 martipe02 2006 1 NYN NL P 23 23 398 7 13 5 0 NA NA NA 86683 martipe02 2007 1 NYN NL P 5 5 84 1 0 0 0 NA NA NA 86684 martipe02 2008 1 NYN NL P 20 20 327 6 17 0 1 NA NA NA 86685 martipe02 2009 1 PHI NL P 9 9 134 1 6 0 1 NA NA NA CS ZR 86668 NA NA 86669 NA NA 86670 NA NA 86671 NA NA 86672 NA NA 86673 NA NA 86674 NA NA 86675 NA NA 86676 NA NA 86677 NA NA 86678 NA NA 86679 NA NA 86680 NA NA 86681 NA NA 86682 NA NA 86683 NA NA 86684 NA NA 86685 NA NA > > # Table of games played by Pete Rose at different positions > with(subset(Fielding, playerID == "rosepe01"), xtabs(G ~ POS)) POS 1B 2B 3B OF 939 628 634 1327 > > # Career total G/PO/A/E/DP for Luis Aparicio > Fielding %>% + filter(playerID == "aparilu01") %>% + select(G, PO, A, E, DP) %>% + summarise_each(funs(sum)) Error: ! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. Backtrace: ▆ 1. ├─... %>% summarise_each(funs(sum)) 2. └─dplyr::summarise_each(., funs(sum)) 3. └─dplyr:::each_defunct("summarise_each()") 4. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed Batting 5.325 0.575 5.922 Package: Lahman Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘FHM-primer.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘FHM-primer.Rmd’ --- re-building ‘hits-by-type.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘hits-by-type.Rmd’ --- re-building ‘payroll.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘payroll.Rmd’ --- re-building ‘run-scoring-trends.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘run-scoring-trends.Rmd’ --- re-building ‘strikeoutsandhr.Rmd’ using rmarkdown Quitting from strikeoutsandhr.Rmd:58-69 [Batting-filter] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. --- Backtrace: ▆ 1. ├─... %>% summarise_each(funs(sum)) 2. └─dplyr::summarise_each(., funs(sum)) 3. └─dplyr:::each_defunct("summarise_each()") 4. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()") 5. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'strikeoutsandhr.Rmd' failed with diagnostics: `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. --- failed re-building ‘strikeoutsandhr.Rmd’ --- re-building ‘vignette-intro.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘vignette-intro.Rmd’ SUMMARY: processing the following file failed: ‘strikeoutsandhr.Rmd’ Error: Vignette re-building failed. Execution halted Package: lookupTable Check: examples New result: ERROR Running examples in ‘lookupTable-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: predict.lookupTable > ### Title: Predictions from a look-up table > ### Aliases: predict.lookupTable > > ### ** Examples > > df.input <- cars > response <- 'dist' > feature.boundaries <- list(c(-Inf, 5, 10, 15, 20, 25, Inf)) > features.con <- c('speed') > dist.table <- lookupTable(df.input, response, feature.boundaries, features.con) Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. Backtrace: ▆ 1. └─lookupTable::lookupTable(...) 2. └─methods::new(``, ...) 3. ├─methods::initialize(value, ...) 4. └─lookupTable (local) initialize(value, ...) 5. └─lookupTable (local) .local(.Object, ...) 6. └─dplyr::summarise_(...) 7. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) Execution halted Package: lookupTable Check: tests New result: ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(lookupTable) Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > > test_check("lookupTable") Saving _problems/test.lookupTable-8.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test.lookupTable.R:8:1'): (code run outside of `test_that()`) ─────── Error: `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. Backtrace: ▆ 1. └─lookupTable::lookupTable(...) at test.lookupTable.R:8:1 2. └─methods::new(``, ...) 3. ├─methods::initialize(value, ...) 4. └─lookupTable (local) initialize(value, ...) 5. └─lookupTable (local) .local(.Object, ...) 6. └─dplyr::summarise_(...) 7. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: ! Test failures. Execution halted Package: ltertools Check: tests New result: ERROR Running ‘testthat.R’ [4s/78s] 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(ltertools) > > test_check("ltertools") Retrieving data for 2022-02-07 Saving _problems/test-solar_day_info-27.R Saving _problems/test-solar_day_info-35.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 35 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-solar_day_info.R:25:3'): Warnings are returned ───────────────── Error in `open.connection(file, "rt")`: cannot open the connection to 'https://api.sunrise-sunset.org/json?lat=34&lng=-119&date=2022-02-07' Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-solar_day_info.R:25:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ltertools::solar_day_info(...) 8. ├─base::suppressWarnings(...) 9. │ └─base::withCallingHandlers(...) 10. └─utils::read.csv(file = url(description = day_query), header = F) 11. └─utils::read.table(...) 12. ├─base::open(file, "rt") 13. └─base::open.connection(file, "rt") ── Error ('test-solar_day_info.R:33:3'): Outputs are correct ─────────────────── Error in `open.connection(file, "rt")`: cannot open the connection to 'https://api.sunrise-sunset.org/json?lat=34&lng=-119&date=2022-02-07' Backtrace: ▆ 1. └─ltertools::solar_day_info(...) at test-solar_day_info.R:33:3 2. ├─base::suppressWarnings(...) 3. │ └─base::withCallingHandlers(...) 4. └─utils::read.csv(file = url(description = day_query), header = F) 5. └─utils::read.table(...) 6. ├─base::open(file, "rt") 7. └─base::open.connection(file, "rt") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 35 ] Error: ! Test failures. Execution halted Package: mantis Check: tests New result: ERROR Running ‘testthat.R’ [35s/36s] 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(mantis) > > test_check("mantis") Saving _problems/test-plots-interactive-21.R Saving _problems/test-plots-interactive-44.R Saving _problems/test-prepare-25.R [ FAIL 3 | WARN 3 | SKIP 3 | PASS 485 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test-plots-static.R:1:1', 'test-plots-static.R:27:1', 'test-plots-static.R:53:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plots-interactive.R:17:3'): output_table_interactive() avoids min/max warnings when all values are NA ── Expected `output_table_interactive(...)` not to throw any warnings. Actually got a with message: There was 1 warning in `dplyr::mutate()`. i In argument: `value_for_history = dplyr::case_when(...)`. i In group 1: `item.item = "na"`. Caused by warning: ! Calling `case_when()` with size 1 LHS inputs and size >1 RHS inputs was deprecated in dplyr 1.2.0. i This `case_when()` statement can result in subtle silent bugs and is very inefficient. Please use a series of if statements instead: ``` # Previously case_when(scalar_lhs1 ~ rhs1, scalar_lhs2 ~ rhs2, .default = default) # Now if (scalar_lhs1) { rhs1 } else if (scalar_lhs2) { rhs2 } else { default } ``` ── Failure ('test-plots-interactive.R:40:3'): output_table_interactive() avoids min/max warnings when all deltas are NA ── Expected `output_table_interactive(...)` not to throw any warnings. Actually got a with message: There was 1 warning in `dplyr::mutate()`. i In argument: `value_for_history = dplyr::case_when(...)`. i In group 1: `item.item = "sparse"`. Caused by warning: ! Calling `case_when()` with size 1 LHS inputs and size >1 RHS inputs was deprecated in dplyr 1.2.0. i This `case_when()` statement can result in subtle silent bugs and is very inefficient. Please use a series of if statements instead: ``` # Previously case_when(scalar_lhs1 ~ rhs1, scalar_lhs2 ~ rhs2, .default = default) # Now if (scalar_lhs1) { rhs1 } else if (scalar_lhs2) { rhs2 } else { default } ``` ── Failure ('test-prepare.R:23:3'): prepare_table() avoids min/max warnings when all values in a group are NA ── Expected `prepare_table(prepared_df, inputspec = inputspec)` not to throw any warnings. Actually got a with message: There were 2 warnings in `dplyr::mutate()`. The first warning was: i In argument: `value_for_history = dplyr::case_when(...)`. i In group 1: `item.item = "na"`. Caused by warning: ! Calling `case_when()` with size 1 LHS inputs and size >1 RHS inputs was deprecated in dplyr 1.2.0. i This `case_when()` statement can result in subtle silent bugs and is very inefficient. Please use a series of if statements instead: ``` # Previously case_when(scalar_lhs1 ~ rhs1, scalar_lhs2 ~ rhs2, .default = default) # Now if (scalar_lhs1) { rhs1 } else if (scalar_lhs2) { rhs2 } else { default } ``` i Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. [ FAIL 3 | WARN 3 | SKIP 3 | PASS 485 ] Error: ! Test failures. Execution halted Package: mapboxapi Check: R code for possible problems New result: NOTE mb_optimized_route: no visible binding for global variable ‘location’ Undefined global functions or variables: location Package: markets Check: R code for possible problems New result: NOTE simulate_quantities_and_prices,simulated_model: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: mde Check: examples New result: ERROR Running examples in ‘mde-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: drop_all_na > ### Title: Drop columns for which all values are NA > ### Aliases: drop_all_na > > ### ** Examples > > test <- data.frame(ID= c("A","A","B","A","B"), Vals = c(rep(NA,4),2)) > test2 <- data.frame(ID= c("A","A","B","A","B"), Vals = rep(NA, 5)) > # drop columns where all values are NA > drop_all_na(test2) ID 1 A 2 A 3 B 4 A 5 B > # drop NAs only if all are NA for a given group, drops group too. > drop_all_na(test, "ID") Error in `dplyr::filter()`: ℹ In argument: `dplyr::across(everything(), ~!all_na(.))`. ℹ In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. Backtrace: ▆ 1. ├─mde::drop_all_na(test, "ID") 2. ├─mde:::drop_all_na.data.frame(test, "ID") 3. │ └─... %>% dplyr::ungroup() 4. ├─dplyr::ungroup(.) 5. ├─dplyr::filter(., dplyr::across(everything(), ~!all_na(.))) 6. ├─dplyr:::filter.data.frame(., dplyr::across(everything(), ~!all_na(.))) 7. │ └─dplyr:::filter_impl(...) 8. │ └─dplyr:::filter_rows(...) 9. │ └─dplyr:::filter_eval(...) 10. │ ├─base::withCallingHandlers(...) 11. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 12. │ └─dplyr (local) eval() 13. ├─dplyr:::dplyr_internal_error(...) 14. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 15. │ └─rlang:::signal_abort(cnd, .file) 16. │ └─base::signalCondition(cnd) 17. └─dplyr (local) ``(``) 18. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: mde Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘mde_vignette.rmd’ using rmarkdown Quitting from mde_vignette.rmd:499-507 [unnamed-chunk-45] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::filter()`: ℹ In argument: `dplyr::across(...)`. ℹ In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. --- Backtrace: ▆ 1. ├─mde::drop_na_if(...) 2. ├─mde:::drop_na_if.data.frame(...) 3. │ └─... %>% dplyr::ungroup() 4. ├─dplyr::ungroup(.) 5. ├─dplyr::filter(...) 6. ├─dplyr:::filter.data.frame(...) 7. │ └─dplyr:::filter_impl(...) 8. │ └─dplyr:::filter_rows(...) 9. │ └─dplyr:::filter_eval(...) 10. │ ├─base::withCallingHandlers(...) 11. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 12. │ └─dplyr (local) eval() 13. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'mde_vignette.rmd' failed with diagnostics: ℹ In argument: `dplyr::across(...)`. ℹ In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. --- failed re-building ‘mde_vignette.rmd’ --- re-building ‘missingness.rmd’ using rmarkdown --- finished re-building ‘missingness.rmd’ --- re-building ‘recoding.rmd’ using rmarkdown Quitting from recoding.rmd:300-308 [unnamed-chunk-25] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::filter()`: ℹ In argument: `dplyr::across(...)`. ℹ In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. --- Backtrace: ▆ 1. ├─mde::drop_na_if(...) 2. ├─mde:::drop_na_if.data.frame(...) 3. │ └─... %>% dplyr::ungroup() 4. ├─dplyr::ungroup(.) 5. ├─dplyr::filter(...) 6. ├─dplyr:::filter.data.frame(...) 7. │ └─dplyr:::filter_impl(...) 8. │ └─dplyr:::filter_rows(...) 9. │ └─dplyr:::filter_eval(...) 10. │ ├─base::withCallingHandlers(...) 11. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 12. │ └─dplyr (local) eval() 13. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'recoding.rmd' failed with diagnostics: ℹ In argument: `dplyr::across(...)`. ℹ In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. --- failed re-building ‘recoding.rmd’ SUMMARY: processing the following files failed: ‘mde_vignette.rmd’ ‘recoding.rmd’ Error: Vignette re-building failed. Execution halted Package: mde Check: tests New result: ERROR Running ‘testthat.R’ [5s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(mde) Welcome to mde. This is mde version 0.3.2. Please file issues and feedback at https://www.github.com/Nelson-Gon/mde/issues Turn this message off using 'suppressPackageStartupMessages(library(mde))' Happy Exploration :) > > test_check("mde") Saving _problems/test_drop_all_na-16.R Saving _problems/test_drop_na_if-39.R Dropped 2 rows. Dropped 2 rows. Dropped 2 rows. [ FAIL 2 | WARN 4 | SKIP 15 | PASS 105 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On CRAN (15): 'test_custom_na_recode.R:1:1', 'test_dict_recode.R:1:1', 'test_drop_na_at.R:1:1', 'test_drop_row_if.R:1:1', 'test_get_na_counts.R:1:1', 'test_na_summary.R:1:1', 'test_percent_missing.R:1:1', 'test_recode_as_na.R:1:1', 'test_recode_as_na_for.R:1:1', 'test_recode_as_na_if.R:1:1', 'test_recode_as_na_str.R:21:1', 'test_recode_as_value.R:1:1', 'test_recode_na_as.R:1:1', 'test_recode_na_if.R:2:1', 'test_sorting_missingness.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_drop_all_na.R:16:13'): drop_all_na errors on absent columns ──── Error in `dplyr::filter(., dplyr::across(everything(), ~!all_na(.)))`: i In argument: `dplyr::across(everything(), ~!all_na(.))`. i In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. i If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_drop_all_na.R:16:13 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(drop_all_na(test, grouping_cols = "ID")) 5. ├─mde::drop_all_na(test, grouping_cols = "ID") 6. ├─mde:::drop_all_na.data.frame(test, grouping_cols = "ID") 7. │ └─... %>% dplyr::ungroup() 8. ├─dplyr::ungroup(.) 9. ├─dplyr::filter(., dplyr::across(everything(), ~!all_na(.))) 10. ├─dplyr:::filter.data.frame(., dplyr::across(everything(), ~!all_na(.))) 11. │ └─dplyr:::filter_impl(...) 12. │ └─dplyr:::filter_rows(...) 13. │ └─dplyr:::filter_eval(...) 14. │ ├─base::withCallingHandlers(...) 15. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 16. │ └─dplyr (local) eval() 17. ├─dplyr:::dplyr_internal_error(...) 18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 19. │ └─rlang:::signal_abort(cnd, .file) 20. │ └─base::signalCondition(cnd) 21. └─dplyr (local) ``(``) 22. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test_drop_na_if.R:37:15'): drop_na_if errors as expected ──────────── Error in `dplyr::filter(., dplyr::across(dplyr::everything(), ~!switches(mean(is.na(.)) * 100, sign = sign, percent_na = percent_na)))`: i In argument: `dplyr::across(...)`. i In group 1: `ID = "A"`. Caused by error: ! `..1` must be a logical vector, not a object. i If you used `across()` to generate this data frame, please use `if_any()` or `if_all()` instead. Backtrace: ▆ 1. ├─mde::drop_na_if(grouped_drop, percent_na = 67, grouping_cols = "ID") at test_drop_na_if.R:37:15 2. ├─mde:::drop_na_if.data.frame(grouped_drop, percent_na = 67, grouping_cols = "ID") 3. │ └─... %>% dplyr::ungroup() 4. ├─dplyr::ungroup(.) 5. ├─dplyr::filter(...) 6. ├─dplyr:::filter.data.frame(...) 7. │ └─dplyr:::filter_impl(...) 8. │ └─dplyr:::filter_rows(...) 9. │ └─dplyr:::filter_eval(...) 10. │ ├─base::withCallingHandlers(...) 11. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 12. │ └─dplyr (local) eval() 13. ├─dplyr:::dplyr_internal_error(...) 14. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 15. │ └─rlang:::signal_abort(cnd, .file) 16. │ └─base::signalCondition(cnd) 17. └─dplyr (local) ``(``) 18. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 2 | WARN 4 | SKIP 15 | PASS 105 ] Error: ! Test failures. Execution halted Package: metamicrobiomeR Check: R code for possible problems New result: NOTE metatab.show: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: MetaNet Check: examples New result: ERROR Running examples in ‘MetaNet-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_group_skeleton > ### Title: Get skeleton network according to a group > ### Aliases: get_group_skeleton c_net_skeleton skeleton_plot > > ### ** Examples > > get_group_skeleton(co_net) -> ske_net Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─MetaNet::get_group_skeleton(co_net) 2. │ ├─base::suppressWarnings(...) 3. │ │ └─base::withCallingHandlers(...) 4. │ └─... %>% .[V(tmp_go)$name, "n"] 5. ├─tibble::column_to_rownames(., Group) 6. │ ├─base::stopifnot(is.data.frame(.data)) 7. │ └─base::is.data.frame(.data) 8. ├─dplyr::count(.) 9. └─dplyr::group_by_(., Group) 10. └─dplyr:::lazy_defunct("group_by") 11. └─lifecycle::deprecate_stop(...) 12. └─lifecycle:::deprecate_stop0(msg) 13. └─rlang::cnd_signal(...) Execution halted Package: metrica Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Cheatsheet.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Cheatsheet.Rmd’ --- re-building ‘JOSS_publication.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘JOSS_publication.Rmd’ --- re-building ‘Shinyapp.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Shinyapp.Rmd’ --- re-building ‘apsim_open.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘apsim_open.Rmd’ --- re-building ‘available_metrics_classification.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘available_metrics_classification.Rmd’ --- re-building ‘available_metrics_regression.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘available_metrics_regression.Rmd’ --- re-building ‘classification_case.Rmd’ using rmarkdown Quitting from classification_case.Rmd:342-353 [multiple_models unnested summarise] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarise()`: ℹ In argument: `metrics_summary(obs = actual, pred = predicted, type = "classification")`. ℹ In group 1: `id = "fold_1"`. Caused by error: ! `metrics_summary(obs = actual, pred = predicted, type = "classification")` must be size 1, not 27. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─... %>% dplyr::arrange(Metric) 2. ├─dplyr::arrange(., Metric) 3. ├─dplyr::summarise(...) 4. ├─dplyr:::summarise.grouped_df(., metrics_summary(obs = actual, pred = predicted, type = "classification")) 5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 6. │ └─base::withCallingHandlers(...) 7. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'classification_case.Rmd' failed with diagnostics: ℹ In argument: `metrics_summary(obs = actual, pred = predicted, type = "classification")`. ℹ In group 1: `id = "fold_1"`. Caused by error: ! `metrics_summary(obs = actual, pred = predicted, type = "classification")` must be size 1, not 27. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘classification_case.Rmd’ --- re-building ‘regression_case.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘regression_case.Rmd’ SUMMARY: processing the following file failed: ‘classification_case.Rmd’ Error: Vignette re-building failed. Execution halted Package: microhaplot Check: examples New result: ERROR Running examples in ‘microhaplot-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: prepHaplotFiles > ### Title: Extracts haplotype from alignment reads. > ### Aliases: prepHaplotFiles > > ### ** Examples > > > run.label <- "sebastes" > > sam.path <- tempdir() > untar(system.file("extdata", + "sebastes_sam.tar.gz", + package="microhaplot"), + exdir = sam.path) > > > label.path <- file.path(sam.path, "label.txt") > vcf.path <- file.path(sam.path, "sebastes.vcf") > > mvShinyHaplot(tempdir()) [1] TRUE > app.path <- file.path(tempdir(), "microhaplot") > > # retrieve system Perl version number > perl.version <- as.numeric(system('perl -e "print $];"', intern=TRUE)) > > if (perl.version >= 5.014) { + haplo.read.tbl <- prepHaplotFiles(run.label = run.label, + sam.path = sam.path, + out.path = tempdir(), + label.path = label.path, + vcf.path = vcf.path, + app.path = app.path) + }else { + message("Perl version is outdated. Must >= 5.014.")} Perl is found in system ...running Hapture.pl to extract haplotype information (takes a while)... Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. ├─microhaplot::prepHaplotFiles(...) 2. │ └─... %>% dplyr::tbl_df() 3. └─dplyr::tbl_df(.) 4. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Package: mixtur Check: examples New result: ERROR Running examples in ‘mixtur-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_error > ### Title: Plot response error of behavioural data relative to target > ### values. > ### Aliases: plot_error > > ### ** Examples > > plot_error(bays2009_full, + unit = "radians", + set_size_var = "set_size") Error in `summarise()`: ℹ In argument: `y = hist(.data$error, breaks = break_points, plot = FALSE)$density`. ℹ In group 1: `id = 1`, `set_size = 1`. Caused by error: ! `y` must be size 1, not 17. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─mixtur::plot_error(bays2009_full, unit = "radians", set_size_var = "set_size") 2. │ └─... %>% ... 3. ├─dplyr::summarise(., mean_error = mean(.data$y), se_error = (sd(.data$y)/sqrt(length(.data$y)))) 4. ├─dplyr::group_by(., .data$set_size, .data$x) 5. ├─dplyr::summarise(...) 6. ├─dplyr:::summarise.grouped_df(...) 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) ``(``) 14. └─dplyr (local) handler(cnd) 15. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: MixviR Check: examples New result: ERROR Running examples in ‘MixviR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: create_ref > ### Title: Create MixVir-formatted reference genome object > ### Aliases: create_ref > ### Keywords: reference > > ### ** Examples > > site1 <- "https://raw.githubusercontent.com/mikesovic/MixviR/main/raw_files/GCF_ASM985889v3.fa" > site2 <- "https://raw.githubusercontent.com/mikesovic/MixviR/main/raw_files/sars_cov2_genes.bed" > > if (httr::http_error(site1) | httr::http_error(site2)) { + message("No internet connection or data source broken.") + return(NULL) + } else { + create_ref( + genome = site1, + feature.bed = site2, + code.num = "1") + } Rows: 12 Columns: 6 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (4): X1, X4, X5, X6 dbl (2): X2, X3 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://raw.githubusercontent.com/mikesovic/MixviR/main/raw_files/GCF_ASM985889v3.fa' Content type 'text/plain; charset=utf-8' length 30290 bytes (29 KB) ================================================== downloaded 29 KB Error in `dplyr::summarise()`: ℹ In argument: `translation = translate_fwd(REF_BASE, code = code.num)`. ℹ In group 1: `GENE = "E"`. Caused by error: ! `translation` must be size 1, not 228. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─MixviR::create_ref(genome = site1, feature.bed = site2, code.num = "1") 2. │ └─... %>% dplyr::pull(translation) 3. ├─dplyr::pull(., translation) 4. ├─dplyr::arrange(., GENE, POS) 5. ├─dplyr::summarise(...) 6. ├─dplyr:::summarise.grouped_df(...) 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) ``(``) 14. └─dplyr (local) handler(cnd) 15. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: mlVAR Check: R code for possible problems New result: NOTE movingWindow: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: mobr Check: R code for possible problems New result: NOTE plot_rarefaction: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: Momocs Check: examples New result: ERROR Running examples in ‘Momocs-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: PCcontrib > ### Title: Shape variation along PC axes > ### Aliases: PCcontrib PCcontrib.PCA > > ### ** Examples > > bot.p <- PCA(efourier(bot, 12)) 'norm=TRUE' is used and this may be troublesome. See ?efourier #Details > PCcontrib(bot.p, nax=1:3) Error: ! `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─Momocs::PCcontrib(bot.p, nax = 1:3) 2. ├─Momocs:::PCcontrib.PCA(bot.p, nax = 1:3) 3. │ └─Momocs:::morphospace2PCA(x, xax = i, yax = 1, pos = pos.i) 4. │ └─dplyr::bind_cols(df_shp, df_trans) %>% ... 5. └─dplyr::mutate_(...) 6. └─dplyr:::lazy_defunct("mutate") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) Execution halted Package: MonteCarlo Check: examples New result: ERROR Running examples in ‘MonteCarlo-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MakeFrame > ### Title: Conversion of MonteCarlo outputs to data.frame. > ### Aliases: MakeFrame > > ### ** Examples > > test_func<-function(n,loc,scale){ + sample<-rnorm(n, loc, scale) + stat<-sqrt(n)*mean(sample)/sd(sample) + decision<-abs(stat)>1.96 + return(list("decision"=decision, "stat"=stat)) + } > > n_grid<-c(50,100,250,500) > loc_grid<-c(0,1) > scale_grid<-c(1,2) > > param_list=list("n"=n_grid, "loc"=loc_grid, "scale"=scale_grid) > erg<-MonteCarlo(func=test_func, nrep=250, param_list=param_list, ncpus=1) Grid of 16 parameter constellations to be evaluated. Progress: | | | 0% | |==== | 6% | |========= | 12% | |============= | 19% | |================== | 25% | |====================== | 31% | |========================== | 38% | |=============================== | 44% | |=================================== | 50% | |======================================= | 56% | |============================================ | 62% | |================================================ | 69% | |==================================================== | 75% | |========================================================= | 81% | |============================================================= | 88% | |================================================================== | 94% | |======================================================================| 100% > df<-MakeFrame(erg) Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE > head(df) n loc scale decision stat 1 50 0 1 0 0.5140555 2 100 0 1 0 0.7036153 3 250 0 1 0 0.5273391 4 500 0 1 0 0.8101010 5 50 1 1 1 9.5673985 6 100 1 1 1 12.2424763 > > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > library(ggplot2) > tbl <- tbl_df(df) Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. └─dplyr::tbl_df(df) 2. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 3. └─lifecycle:::deprecate_stop0(msg) 4. └─rlang::cnd_signal(...) Execution halted Package: MonteCarlo Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘MonteCarlo-Vignette.Rmd’ using rmarkdown Quitting from MonteCarlo-Vignette.Rmd:315-320 [unnamed-chunk-15] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- Backtrace: ▆ 1. └─dplyr::tbl_df(df) 2. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 3. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'MonteCarlo-Vignette.Rmd' failed with diagnostics: `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- failed re-building ‘MonteCarlo-Vignette.Rmd’ SUMMARY: processing the following file failed: ‘MonteCarlo-Vignette.Rmd’ Error: Vignette re-building failed. Execution halted Package: moodleR Check: R code for possible problems New result: NOTE mdl_courses: no visible binding for global variable ‘id’ mdl_create_cache: no visible binding for global variable ‘id’ mdl_users: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: mpathr Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [10s/10s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(mpathr) > > test_check("mpathr") Saving _problems/test-read_mpath-15.R Saving _problems/test-read_mpath-271.R Saving _problems/test-read_mpath-304.R Saving _problems/test-read_mpath-336.R [ FAIL 4 | WARN 10 | SKIP 0 | PASS 243 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-read_mpath.R:10:3'): Data is imported with no warnings ─────── Expected `read_mpath(file = basic_path, meta_data = meta_path)` not to throw any warnings. Actually got a with message: There was 1 warning in `mutate()`. i In argument: `type = case_match(...)`. Caused by warning: ! `case_match()` was deprecated in dplyr 1.2.0. i Please use `recode_values()` instead. ── Failure ('test-read_mpath.R:265:3'): no warnings are printen when warn_changed_columns is false ── Expected `read_mpath(file = basic_file, meta_data = meta_file, warn_changed_columns = FALSE)` not to throw any warnings. Actually got a with message: There was 1 warning in `mutate()`. i In argument: `type = case_match(...)`. Caused by warning: ! `case_match()` was deprecated in dplyr 1.2.0. i Please use `recode_values()` instead. ── Failure ('test-read_mpath.R:304:3'): meta_data changed columns warnings are limited to 50 ── Expected `out` to have length 51. Actual length: 1. ── Failure ('test-read_mpath.R:336:3'): meta_data limits warnings from reading in meta data files to 50 ── Expected `out` to have length 51. Actual length: 1. [ FAIL 4 | WARN 10 | SKIP 0 | PASS 243 ] Error: ! Test failures. Execution halted Package: mregions2 Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘mregions2.Rmd’ using rmarkdown Quitting from mregions2.Rmd:145-151 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `FUN()`: ! HTTP 500 Internal Server Error. --- Backtrace: ▆ 1. ├─mregions2::gaz_search_by_type("Town") 2. ├─mregions2:::gaz_search_by_type.character("Town") 3. │ ├─... %>% new_mr_df() 4. │ └─base::lapply(x, gaz_rest_records_by_type, ...) 5. │ └─mregions2 (local) FUN(X[[i]], ...) 6. ├─mregions2:::new_mr_df(.) 7. │ ├─base::stopifnot(is.data.frame(x)) 8. │ └─base::is.data.frame(x) 9. └─dplyr::bind_rows(.) 10. └─rlang::list2(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'mregions2.Rmd' failed with diagnostics: HTTP 500 Internal Server Error. --- failed re-building ‘mregions2.Rmd’ SUMMARY: processing the following file failed: ‘mregions2.Rmd’ Error: Vignette re-building failed. Execution halted Package: MSiP Check: examples New result: ERROR Running examples in ‘MSiP-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Weighted.matrixModel > ### Title: Weighted.matrixModel > ### Aliases: Weighted.matrixModel > > ### ** Examples > > data(SampleDatInput) > datScoring <- Weighted.matrixModel(SampleDatInput) Error: ! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. Backtrace: ▆ 1. ├─MSiP::Weighted.matrixModel(SampleDatInput) 2. │ └─... %>% dplyr::select(-1) 3. ├─dplyr::select(., -1) 4. ├─base (local) set_rownames(., .$Experiment.id) 5. │ └─base::is.data.frame(x) 6. ├─base::as.data.frame(.) 7. └─dplyr::summarise_each(., funs(max(.))) 8. └─dplyr:::each_defunct("summarise_each()") 9. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()") 10. └─lifecycle:::deprecate_stop0(msg) 11. └─rlang::cnd_signal(...) Execution halted Package: MSiP Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘MSiP_tutorial.Rmd’ using knitr Quitting from MSiP_tutorial.Rmd:45-49 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. --- Backtrace: ▆ 1. ├─MSiP::diceCoefficient(SampleDatInput) 2. │ ├─base::suppressWarnings(...) 3. │ │ └─base::withCallingHandlers(...) 4. │ └─... %>% dplyr::select(-1) 5. ├─dplyr::select(., -1) 6. └─dplyr::summarise_each(., funs(max(.))) 7. └─dplyr:::each_defunct("summarise_each()") 8. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()") 9. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'MSiP_tutorial.Rmd' failed with diagnostics: `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. --- failed re-building ‘MSiP_tutorial.Rmd’ SUMMARY: processing the following file failed: ‘MSiP_tutorial.Rmd’ Error: Vignette re-building failed. Execution halted Package: mvMAPIT Check: R code for possible problems New result: NOTE mvmapit: no visible binding for global variable ‘id’ simulate_traits: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: NBDCtools Check: R code for possible problems New result: NOTE shadow_replace_binding_missing: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: nfl4th Check: R code for possible problems New result: NOTE get_4th_plays: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: OnboardClient Check: R code for possible problems New result: NOTE get_metadata: no visible binding for global variable ‘id’ get_point_types: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: oncomsm Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘avoiding-bias.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘avoiding-bias.Rmd’ --- re-building ‘oncomsm.Rmd’ using rmarkdown Quitting from oncomsm.Rmd:256-272 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `summarize()`: ℹ In argument: `dt = t - lag(t)`. ℹ In group 1: `iter = 1`, `group_id = "A"`, `subject_id = "ID00827488"`. Caused by error: ! `dt` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─... %>% ... 2. ├─dplyr::summarize(., `median transition time` = median(dt), .groups = "drop") 3. ├─dplyr::group_by(., group_id, from, to) 4. ├─dplyr::filter(., to != "stable") 5. ├─dplyr::summarize(...) 6. ├─dplyr:::summarise.grouped_df(., dt = t - lag(t), from = lag(state), to = state, .groups = "drop") 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: ℹ In argument: `dt = t - lag(t)`. ℹ In group 1: `iter = 1`, `group_id = "A"`, `subject_id = "ID00827488"`. Caused by error: ! `dt` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘oncomsm.Rmd’ --- re-building ‘prior-choice.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘prior-choice.Rmd’ SUMMARY: processing the following file failed: ‘oncomsm.Rmd’ Error: Vignette re-building failed. Execution halted Package: OpenLand Check: R code for possible problems New result: NOTE netgrossplot: no visible binding for global variable ‘changes’ Undefined global functions or variables: changes Package: oRus Check: R code for possible problems New result: NOTE parseRelatedStories: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: pammtools Check: R code for possible problems New result: NOTE sim_pexp: no visible binding for global variable ‘id’ sim_pexp_cr: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: panelr Check: tests New result: ERROR Running ‘testthat.R’ [63s/63s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(panelr) Loading required package: lme4 Loading required package: Matrix Attaching package: 'panelr' The following object is masked from 'package:stats': filter > > test_check("panelr") Saving _problems/test-utils-33.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 409 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-utils.R:33:3'): dplyr functions return panel_data objects ────── Error: `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-utils.R:32:3 2. │ └─base::withCallingHandlers(...) 3. ├─testthat::expect_s3_class(mutate_(w, gender = "fem"), "panel_data") at test-utils.R:33:3 4. │ └─testthat::quasi_label(enquo(object)) 5. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 6. └─dplyr::mutate_(w, gender = "fem") 7. └─dplyr:::lazy_defunct("mutate") 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 409 ] Error: ! Test failures. Execution halted Package: PaRe Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Documentation.Rmd’ using rmarkdown Quitting from Documentation.Rmd:263-268 [lintScore] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `dplyr::summarise()`: ℹ In argument: `.data$type`. Caused by error: ! `.data$type` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─PaRe::lintScore(repo = repo, messages = messages) 2. │ └─... %>% ... 3. ├─dplyr::summarise(...) 4. ├─dplyr:::summarise.data.frame(., .data$type, pct = round(.data$n/nLines * 100, 2)) 5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 6. │ └─base::withCallingHandlers(...) 7. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Documentation.Rmd' failed with diagnostics: ℹ In argument: `.data$type`. Caused by error: ! `.data$type` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘Documentation.Rmd’ SUMMARY: processing the following file failed: ‘Documentation.Rmd’ Error: Vignette re-building failed. Execution halted Package: parSim Check: R code for possible problems New result: NOTE parSim_dt: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: pctax Check: R code for possible problems New result: NOTE plot.time_cm: no visible binding for global variable ‘id’ plot_two_tree: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: PEIMAN2 Check: R code for possible problems New result: NOTE psea2mass: no visible binding for global variable ‘id’ sea2mass: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: pems.utils Check: dependencies in R code New result: WARNING Missing or unexported objects: ‘dplyr::rename_vars’ ‘dplyr::select_vars’ Package: petrinetR Check: R code for possible problems New result: NOTE enabled: no visible binding for global variable ‘id’ label: no visible binding for global variable ‘id’ read_PN: no visible binding for global variable ‘id’ rename_places: no visible binding for global variable ‘id’ rename_transitions: no visible binding for global variable ‘id’ render_PN: no visible binding for global variable ‘id’ visNetwork_from_PN: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: pkggraph Check: examples New result: ERROR Running examples in ‘pkggraph-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_all_dependencies > ### Title: get_all_dependencies > ### Aliases: get_all_dependencies > > ### ** Examples > > pkggraph::init(local = TRUE) Using 'local' data ... To fetch data from CRAN over internet, run:`pkggraph::init(local = FALSE)` Done! > # general use > pkggraph::get_all_dependencies("mlr") Error: ! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. └─pkggraph::get_all_dependencies("mlr") 2. └─dplyr::arrange_(res, "relation") 3. └─dplyr:::lazy_defunct("arrange") 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Package: pkggraph Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette_pkggraph.Rmd’ using rmarkdown Quitting from vignette_pkggraph.Rmd:33-58 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. └─pkggraph::get_neighborhood("mlr") 2. ├─dplyr::bind_rows(...) 3. │ └─rlang::list2(...) 4. └─pkggraph::get_all_dependencies(...) 5. └─dplyr::arrange_(res, "relation") 6. └─dplyr:::lazy_defunct("arrange") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'vignette_pkggraph.Rmd' failed with diagnostics: `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘vignette_pkggraph.Rmd’ SUMMARY: processing the following file failed: ‘vignette_pkggraph.Rmd’ Error: Vignette re-building failed. Execution halted Package: placer Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘PlAcER.Rmd’ using rmarkdown Quitting from PlAcER.Rmd:51-57 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- Backtrace: ▆ 1. ├─ctern[1:10, ] %>% tbl_df %>% select(-nest_code) %>% ... 2. ├─knitr::kable(...) 3. ├─dplyr::select(., -nest_code) 4. └─dplyr::tbl_df(.) 5. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PlAcER.Rmd' failed with diagnostics: `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- failed re-building ‘PlAcER.Rmd’ SUMMARY: processing the following file failed: ‘PlAcER.Rmd’ Error: Vignette re-building failed. Execution halted Package: plotBart Check: examples New result: ERROR Running examples in ‘plotBart-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_balance > ### Title: Plot the balance > ### Aliases: plot_balance > > ### ** Examples > > data(lalonde) > plot_balance(lalonde, 'treat', c('re78', 'age', 'educ')) + labs(title = 'My new title') Error in `summarize()`: ℹ In argument: `diff = mean - lag(mean)`. ℹ In group 1: `name = "age"`. Caused by error: ! `diff` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─plotBart::plot_balance(lalonde, "treat", c("re78", "age", "educ")) 2. │ └─... %>% ggplot(aes(x = diff, y = name, color = abs(diff))) 3. ├─ggplot2::ggplot(., aes(x = diff, y = name, color = abs(diff))) 4. ├─stats::na.omit(.) 5. ├─dplyr::summarize(., diff = mean - lag(mean), .groups = "drop") 6. ├─dplyr:::summarise.grouped_df(., diff = mean - lag(mean), .groups = "drop") 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) ``(``) 14. └─dplyr (local) handler(cnd) 15. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: plotBart Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘modifying-plots.Rmd’ using rmarkdown Quitting from modifying-plots.Rmd:23-33 [setup] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `summarize()`: ℹ In argument: `diff = mean - lag(mean)`. ℹ In group 1: `name = "age"`. Caused by error: ! `diff` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace: ▆ 1. ├─plotBart::plot_balance(...) 2. │ └─... %>% ggplot(aes(x = diff, y = name, color = abs(diff))) 3. ├─ggplot2::ggplot(., aes(x = diff, y = name, color = abs(diff))) 4. ├─stats::na.omit(.) 5. ├─dplyr::summarize(., diff = mean - lag(mean), .groups = "drop") 6. ├─dplyr:::summarise.grouped_df(., diff = mean - lag(mean), .groups = "drop") 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'modifying-plots.Rmd' failed with diagnostics: ℹ In argument: `diff = mean - lag(mean)`. ℹ In group 1: `name = "age"`. Caused by error: ! `diff` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘modifying-plots.Rmd’ SUMMARY: processing the following file failed: ‘modifying-plots.Rmd’ Error: Vignette re-building failed. Execution halted Package: plotBart Check: tests New result: ERROR Running ‘testthat.R’ [97s/82s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(vdiffr) > library(plotBart) Loading required package: bartCause Loading required package: ggplot2 > > test_check("plotBart") # run tests fitting treatment model via method 'bart' fitting response model via method 'bart' fitting treatment model via method 'bart' fitting response model via method 'bart' fitting treatment model via method 'bart' fitting response model via method 'bart' Saving _problems/test_plots-20.R [ FAIL 1 | WARN 3 | SKIP 0 | PASS 5 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_plots.R:20:1'): (code run outside of `test_that()`) ──────────── Error in `summarize(., diff = mean - lag(mean), .groups = "drop")`: ℹ In argument: `diff = mean - lag(mean)`. ℹ In group 1: `name = "age"`. Caused by error: ! `diff` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─plotBart::plot_balance(...) at test_plots.R:20:1 2. │ └─... %>% ggplot(aes(x = diff, y = name, color = abs(diff))) 3. ├─ggplot2::ggplot(., aes(x = diff, y = name, color = abs(diff))) 4. ├─stats::na.omit(.) 5. ├─dplyr::summarize(., diff = mean - lag(mean), .groups = "drop") 6. ├─dplyr:::summarise.grouped_df(., diff = mean - lag(mean), .groups = "drop") 7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 8. │ └─base::withCallingHandlers(...) 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) ``(``) 14. └─dplyr (local) handler(cnd) 15. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 1 | WARN 3 | SKIP 0 | PASS 5 ] Deleting unused snapshots: 'plots/balance.svg', 'plots/cate.svg', 'plots/mod-c-loess.svg', 'plots/mod-c-pd.svg', 'plots/mod-d-density.svg', 'plots/mod-d-linerange.svg', 'plots/mod-search.svg', 'plots/overlappscoresdensity.svg', 'plots/overlappscoreshist.svg', 'plots/overlapvarsdensity.svg', 'plots/overlapvarshist.svg', 'plots/pate.svg', 'plots/sate.svg', 'plots/supportchi.svg', 'plots/supportnone.svg', 'plots/supportsd.svg', 'plots/trace.svg', 'plots/waterfall1.svg', and 'plots/waterfall2.svg' Error: ! Test failures. Execution halted Package: plotor Check: tests New result: ERROR Running ‘testthat.R’ [44s/44s] 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(plotor) > > test_check("plotor") Saving _problems/test-plot_or-250.R Saving _problems/test-plot_or-293.R [ FAIL 2 | WARN 1 | SKIP 0 | PASS 74 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plot_or.R:250:3'): `assumption_no_multicollinearity()` works as expected ── Expected `lr <- get_lr_infert()` to run silently. Actual noise: warnings. ── Failure ('test-plot_or.R:290:3'): `assumption_sample_size()` works as expected ── Expected `{ ... }` to run silently. Actual noise: warnings. [ FAIL 2 | WARN 1 | SKIP 0 | PASS 74 ] Error: ! Test failures. Execution halted Package: processmapR Check: R code for possible problems New result: NOTE render_map: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: psrwe Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘ps_matching.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘ps_matching.Rmd’ --- re-building ‘pskm_rct.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘pskm_rct.Rmd’ --- re-building ‘pskm_single.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘pskm_single.Rmd’ --- re-building ‘vignette.Rmd’ using rmarkdown Quitting from vignette.Rmd:45-47 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The `.dots` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. --- Backtrace: ▆ 1. ├─base::plot(dta_ps, plot_type = "balance") 2. ├─base::plot(dta_ps, plot_type = "balance") 3. ├─psrwe:::plot.PSRWE_DTA(dta_ps, plot_type = "balance") 4. │ └─psrwe:::plot_balance(x, ...) 5. │ └─psrwe:::plot_balance_fac(...) 6. │ └─psrwe:::get_freq_tbl(...) 7. │ └─... %>% rename(Value = v) 8. ├─dplyr::rename(., Value = v) 9. ├─dplyr::mutate(., Cov = v) 10. ├─dplyr::mutate_if(., is.factor, as.character) 11. │ └─dplyr:::check_grouped(.tbl, "mutate", "if") 12. │ └─dplyr::is_grouped_df(tbl) 13. ├─dplyr::ungroup(.) 14. ├─dplyr::mutate(., Sum = sum(.data$n), Freq = .data$n/sum(.data$n)) 15. ├─dplyr::group_by(., !!as.name(var_groupby)) 16. ├─dplyr::count(., .dots = c(var_groupby, v)) 17. └─dplyr:::count.data.frame(., .dots = c(var_groupby, v)) 18. ├─dplyr::group_by(x, ..., .add = TRUE, .drop = .drop) 19. └─dplyr:::group_by.data.frame(x, ..., .add = TRUE, .drop = .drop) 20. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) 21. └─lifecycle::deprecate_stop("1.0.0", "group_by(.dots = )") 22. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'vignette.Rmd' failed with diagnostics: The `.dots` argument of `group_by()` was deprecated in dplyr 1.0.0 and is now defunct. --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Package: psycho Check: examples New result: ERROR Running examples in ‘psycho-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: assess > ### Title: Compare a patient's score to a control group > ### Aliases: assess > > ### ** Examples > > result <- assess(patient = 124, mean = 100, sd = 15, n = 100) Error: ! `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─psycho::assess(patient = 124, mean = 100, sd = 15, n = 100) 2. │ └─psycho::crawford.test(...) 3. │ └─... %>% ggplot(aes_string(x = "x", ymin = 0, ymax = "y")) 4. ├─ggplot2::ggplot(., aes_string(x = "x", ymin = 0, ymax = "y")) 5. └─dplyr::mutate_(., x = "scales::rescale(x, from=c(0, 1), to = c(sample_mean, sample_mean+sample_sd))") 6. └─dplyr:::lazy_defunct("mutate") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) Execution halted Package: psycho Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(psycho) > > test_check("psycho") Saving _problems/test-assess-10.R Saving _problems/test-assess-45.R The Crawford-Howell (1998) t-test suggests no dissociation between test X and test Y (t(5) = 2.10, p p = 0.090). The patient's score on test X is not significantly altered compared to its score on test Y. .0.00% .33.00% .67.00% .100.00% 1 [ FAIL 2 | WARN 0 | SKIP 0 | PASS 17 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-assess.R:7:3'): assess ───────────────────────────────────────── Error: `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─psycho::assess(...) at test-assess.R:7:3 2. │ └─psycho::crawford.test(...) 3. │ └─... %>% ggplot(aes_string(x = "x", ymin = 0, ymax = "y")) 4. ├─ggplot2::ggplot(., aes_string(x = "x", ymin = 0, ymax = "y")) 5. └─dplyr::mutate_(., x = "scales::rescale(x, from=c(0, 1), to = c(sample_mean, sample_mean+sample_sd))") 6. └─dplyr:::lazy_defunct("mutate") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) ── Error ('test-assess.R:42:3'): crawford.test ───────────────────────────────── Error: `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `mutate()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─psycho::crawford.test(...) at test-assess.R:42:3 2. │ └─... %>% ggplot(aes_string(x = "x", ymin = 0, ymax = "y")) 3. ├─ggplot2::ggplot(., aes_string(x = "x", ymin = 0, ymax = "y")) 4. └─dplyr::mutate_(., x = "scales::rescale(x, from=c(0, 1), to = c(sample_mean, sample_mean+sample_sd))") 5. └─dplyr:::lazy_defunct("mutate") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 17 ] Error: ! Test failures. Execution halted Package: quickpsy Check: examples New result: ERROR Running examples in ‘quickpsy-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: deviance > ### Title: Calculates the deviances > ### Aliases: deviance > > ### ** Examples > > library(MPDiR) # contains the Vernier data > fit <- quickpsy(Vernier, Phaseshift, NumUpward, N, + grouping = .(Direction, WaveForm, TempFreq), B = 20) Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─quickpsy::quickpsy(...) 2. │ └─quickpsy::quickpsy_(...) 3. │ └─quickpsy::fitpsy(...) 4. │ └─d %>% group_by_(.dots = groups) 5. └─dplyr::group_by_(., .dots = groups) 6. └─dplyr:::lazy_defunct("group_by") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) Execution halted Package: RcmdrPlugin.RiskDemo Check: whether package can be installed New result: ERROR Installation failed. Package: refund.shiny Check: R code for possible problems New result: NOTE plot_shiny.flcm : : no visible binding for global variable ‘id’ plot_shiny.fpca : : no visible binding for global variable ‘id’ plot_shiny.registration : : no visible binding for global variable ‘id’ registerLasagna: no visible binding for global variable ‘id’ thin_functional_data: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: rollmatch Check: examples New result: ERROR Running examples in ‘rollmatch-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: rollmatch > ### Title: Rolling entry matching > ### Aliases: rollmatch > > ### ** Examples > > data(package="rollmatch", "rem_synthdata_small") > reduced_data <- reduce_data(data = rem_synthdata_small, treat = "treat", + tm = "quarter", entry = "entry_q", + id = "indiv_id", lookback = 1) > fm <- as.formula(treat ~ qtr_pmt + yr_pmt + age) > vars <- all.vars(fm) > scored_data <- score_data(reduced_data = reduced_data, + model_type = "logistic", match_on = "logit", + fm = fm, treat = "treat", + tm = "quarter", entry = "entry_q", id = "indiv_id") > output <- rollmatch(scored_data, data=rem_synthdata_small, treat = "treat", + tm = "quarter", entry = "entry_q", id = "indiv_id", + vars = vars, lookback = 1, alpha = .2, + standard_deviation = "average", num_matches = 3, + replacement = TRUE) Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─rollmatch::rollmatch(...) 2. │ └─rollmatch:::add_balance_table(...) 3. │ └─scored_data[, vars] %>% dplyr::group_by_(treat) 4. └─dplyr::group_by_(., treat) 5. └─dplyr:::lazy_defunct("group_by") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: rpivotTable Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘NEWS.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘NEWS.Rmd’ --- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown Quitting from rpivotTableIntroduction.Rmd:102-110 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- Backtrace: ▆ 1. ├─... %>% ... 2. ├─rpivotTable::rpivotTable(., rows = "Sepal.Width", rendererName = "Treemap") 3. │ └─base::intersect(...) 4. ├─dplyr::filter(., Sepal.Width > 3 & Sepal.Length > 5) 5. └─dplyr::tbl_df(.) 6. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 7. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics: `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. --- failed re-building ‘rpivotTableIntroduction.Rmd’ SUMMARY: processing the following file failed: ‘rpivotTableIntroduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: rpivotTable Check: tests New result: ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(rpivotTable) > > test_check("rpivotTable") Saving _problems/test_data-25.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_data.R:22:3'): data is not changed ───────────────────────────── Error: `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. ├─testthat::expect_is(rpivotTable(tbl_df(iris))$x$data, "tbl_df") at test_data.R:22:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─rpivotTable::rpivotTable(tbl_df(iris)) 5. │ └─base::intersect(...) 6. └─dplyr::tbl_df(iris) 7. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] Error: ! Test failures. Execution halted Package: rprev Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘diagnostics.Rmd’ using rmarkdown Quitting from diagnostics.Rmd:214-216 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─base::plot(prevsurv) 2. ├─rprev:::plot.survfit.prev(prevsurv) 3. │ └─... %>% dplyr::arrange_("time") 4. └─dplyr::arrange_(., "time") 5. └─dplyr:::lazy_defunct("arrange") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'diagnostics.Rmd' failed with diagnostics: `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘diagnostics.Rmd’ --- re-building ‘user_guide.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘user_guide.Rmd’ SUMMARY: processing the following file failed: ‘diagnostics.Rmd’ Error: Vignette re-building failed. Execution halted Package: scistreer Check: R code for possible problems New result: NOTE annotate_tree: no visible binding for global variable ‘id’ label_edges: no visible binding for global variable ‘id’ mut_to_tree: no visible binding for global variable ‘id’ transfer_links: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: scSpatialSIM Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a01_Introduction.Rmd’ using rmarkdown Quitting from a01_Introduction.Rmd:148-155 [unnamed-chunk-13] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `combine_vars()`: ! Faceting variables must have at least one value. --- Backtrace: ▆ 1. ├─base::withVisible(knit_print(x, ...)) 2. ├─knitr::knit_print(x, ...) 3. └─knitr:::knit_print.default(x, ...) 4. └─knitr::normal_print(x) 5. ├─base::print(x) 6. └─ggplot2 (local) `print.ggplot2::ggplot`(x) 7. ├─ggplot2::ggplot_build(x) 8. └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x) 9. └─layout$setup(data, plot@data, plot@plot_env) 10. └─ggplot2 (local) setup(..., self = self) 11. └─self$facet$compute_layout(data, self$facet_params) 12. └─ggplot2 (local) compute_layout(..., self = self) 13. └─ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a01_Introduction.Rmd' failed with diagnostics: Faceting variables must have at least one value. --- failed re-building ‘a01_Introduction.Rmd’ --- re-building ‘a02_Using_with_spatialTIME.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘a02_Using_with_spatialTIME.Rmd’ SUMMARY: processing the following file failed: ‘a01_Introduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: servosphereR Check: R code for possible problems New result: NOTE aggregateData : : no visible binding for global variable ‘id’ summaryAvgVelocity : : no visible binding for global variable ‘id’ summaryNetDisplacement : : no visible binding for global variable ‘id’ summaryStops : : no visible binding for global variable ‘id’ summaryTotalDistance : : no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: sfc Check: examples New result: ERROR Running examples in ‘sfc-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: sfc > ### Title: Substance Flow Computation > ### Aliases: sfc > > ### ** Examples > > library(sfc) > > ## model as txt > data <- system.file("extdata", "data_utf8.csv", package = "sfc") > model <- system.file("extdata", "model_utf8.txt", package = "sfc") > sfc(data, model, sample.size = 100, fileEncoding = "UTF-8") Read 12 items Error: ! `mutate_each()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `across()` instead. Backtrace: ▆ 1. ├─sfc::sfc(data, model, sample.size = 100, fileEncoding = "UTF-8") 2. │ └─sfc:::impute_data(data) 3. │ └─... %>% mutate_each(funs(as.character(.))) 4. └─dplyr::mutate_each(., funs(as.character(.))) 5. └─dplyr:::each_defunct("mutate_each()") 6. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()") 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: sfo Check: examples New result: ERROR Running examples in ‘sfo-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: sankey_ly > ### Title: Sankey Plot with Plotly > ### Aliases: sankey_ly > > ### ** Examples > > data("sfo_passengers") > > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > > d <- sfo_passengers %>% + filter(activity_period >= 202201 & activity_period < 202301) > > head(d) activity_period operating_airline operating_airline_iata_code 1 202212 EVA Airways BR 2 202212 EVA Airways BR 3 202212 Emirates EK 4 202212 Emirates EK 5 202212 Flair Airlines, Ltd. F8 6 202212 Flair Airlines, Ltd. F8 published_airline published_airline_iata_code geo_summary geo_region 1 EVA Airways BR International Asia 2 EVA Airways BR International Asia 3 Emirates EK International Middle East 4 Emirates EK International Middle East 5 Flair Airlines, Ltd. F8 International Canada 6 Flair Airlines, Ltd. F8 International Canada activity_type_code price_category_code terminal boarding_area 1 Deplaned Other International G 2 Enplaned Other International G 3 Deplaned Other International A 4 Enplaned Other International A 5 Deplaned Low Fare International A 6 Enplaned Low Fare International A passenger_count 1 12405 2 15151 3 13131 4 14985 5 2543 6 2883 > > d %>% + filter(operating_airline == "United Airlines") %>% + mutate(terminal = ifelse(terminal == "International", "international", terminal)) %>% + group_by(operating_airline,activity_type_code, geo_summary, geo_region, terminal) %>% + summarise(total = sum(passenger_count), .groups = "drop") %>% + sankey_ly(cat_cols = c("operating_airline", "terminal","geo_summary", + "geo_region", "activity_type_code"), + num_col = "total", + title = "Distribution of United Airlines Passengers at SFO During 2022") Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. Backtrace: ▆ 1. ├─... %>% ... 2. ├─sfo::sankey_ly(...) 3. │ ├─... %>% dplyr::bind_rows() 4. │ └─base::lapply(...) 5. │ └─sfo (local) FUN(X[[i]], ...) 6. │ └─... %>% ... 7. ├─dplyr::bind_rows(.) 8. │ └─rlang::list2(...) 9. ├─dplyr::left_join(...) 10. ├─dplyr::left_join(...) 11. └─dplyr::summarise_(...) 12. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 13. └─lifecycle::deprecate_stop(...) 14. └─lifecycle:::deprecate_stop0(msg) 15. └─rlang::cnd_signal(...) Execution halted Package: sfo Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘v1_intro.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘v1_intro.Rmd’ --- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown Quitting from v3_analyzing_landing.Rmd:127-143 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. --- Backtrace: ▆ 1. ├─... %>% ... 2. ├─sfo::sankey_ly(...) 3. │ ├─... %>% dplyr::bind_rows() 4. │ └─base::lapply(...) 5. │ └─sfo (local) FUN(X[[i]], ...) 6. │ └─... %>% ... 7. ├─dplyr::bind_rows(.) 8. │ └─rlang::list2(...) 9. ├─dplyr::left_join(...) 10. ├─dplyr::left_join(...) 11. └─dplyr::summarise_(...) 12. └─dplyr:::lazy_defunct("summarise", hint = FALSE) 13. └─lifecycle::deprecate_stop(...) 14. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics: `summarise_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `summarise()` instead. --- failed re-building ‘v3_analyzing_landing.Rmd’ SUMMARY: processing the following file failed: ‘v3_analyzing_landing.Rmd’ Error: Vignette re-building failed. Execution halted Package: shinyloadtest Check: R code for possible problems New result: NOTE load_runs : : no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: SIBER Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Centroid-Vectors.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Centroid-Vectors.Rmd’ --- re-building ‘Customising-Plots-Manually.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Customising-Plots-Manually.Rmd’ --- re-building ‘Ellipse-Overlap.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Ellipse-Overlap.Rmd’ --- re-building ‘Introduction-to-SIBER.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Introduction-to-SIBER.Rmd’ --- re-building ‘Plot-SIA-ggplot2.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Plot-SIA-ggplot2.Rmd’ --- re-building ‘Plot-posterior-ellipses.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Plot-posterior-ellipses.Rmd’ --- re-building ‘Points-Inside-Outside-Ellipse.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Points-Inside-Outside-Ellipse.Rmd’ --- re-building ‘Test-convergence.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Test-convergence.Rmd’ --- re-building ‘kapow-example.Rmd’ using rmarkdown Quitting from kapow-example.Rmd:90-131 [make-packs] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `purrr::map()`: ℹ In index: 1. ℹ With name: 11. Caused by error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─purrr::map(...) 2. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 3. │ ├─purrr:::with_indexed_errors(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ ├─purrr:::call_with_cleanup(...) 6. │ └─SIBER (local) .f(.x[[i]], ...) 7. │ └─... %>% do(calcBoundaries(.data)) 8. ├─dplyr::do(., calcBoundaries(.data)) 9. └─dplyr::group_by_(., .dots = group) 10. └─dplyr:::lazy_defunct("group_by") 11. └─lifecycle::deprecate_stop(...) 12. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'kapow-example.Rmd' failed with diagnostics: ℹ In index: 1. ℹ With name: 11. Caused by error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘kapow-example.Rmd’ --- re-building ‘siber-comparing-communities.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘siber-comparing-communities.Rmd’ --- re-building ‘siber-comparing-populations.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘siber-comparing-populations.Rmd’ SUMMARY: processing the following file failed: ‘kapow-example.Rmd’ Error: Vignette re-building failed. Execution halted Package: simPH Check: examples New result: ERROR Running examples in ‘simPH-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MinMaxLines > ### Title: Transform the simulation object to include only the min and max > ### of the constricted intervals, as well as the lower and upper bounds > ### of the middle 50 percent of the constricted intervals > ### Aliases: MinMaxLines > ### Keywords: internals > > ### ** Examples > > # Load Carpenter (2002) data > data("CarpenterFdaData") > > # Load survival package > library(survival) > > # Run basic model > M1 <- coxph(Surv(acttime, censor) ~ prevgenx + lethal + + deathrt1 + acutediz + hosp01 + hhosleng + + mandiz01 + femdiz01 + peddiz01 + orphdum + + vandavg3 + wpnoavg3 + condavg3 + orderent + + stafcder, data = CarpenterFdaData) > > # Simulate Hazard Ratios > Sim1 <- coxsimLinear(M1, b = "stafcder", + Xj = c(1237, 1600), + Xl = c(1000, 1000), + qi = "Hazard Ratio", + spin = TRUE, ci = 0.99) > > # Find summary statistics of the constricted interval > Sum <- MinMaxLines(Sim1, clean = TRUE) Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. └─simPH::MinMaxLines(Sim1, clean = TRUE) 2. └─dplyr::group_by_(df, .dots = byVars) 3. └─dplyr:::lazy_defunct("group_by") 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Package: simpr Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'reexports.Rd': ‘[dplyr:se-deprecated]{arrange_}’ ‘[dplyr:se-deprecated]{distinct_}’ ‘[dplyr:se-deprecated]{do_}’ ‘[dplyr:se-deprecated]{filter_}’ ‘[dplyr:se-deprecated]{group_by_}’ ‘[dplyr:se-deprecated]{group_indices_}’ ‘[dplyr:se-deprecated]{mutate_}’ ‘[dplyr:se-deprecated]{rename_}’ ‘[dplyr:se-deprecated]{select_}’ ‘[dplyr:se-deprecated]{slice_}’ ‘[dplyr:se-deprecated]{summarise_}’ ‘[dplyr:se-deprecated]{transmute_}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: simts Check: examples New result: ERROR Running examples in ‘simts-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: best_model > ### Title: Select the Best Model > ### Aliases: best_model > > ### ** Examples > > > set.seed(18) > xt = gen_arima(N=100, ar=0.3, d=1, ma=0.3) > x = select_arima(xt, d=1L) > best_model(x, ic = "aic") Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─simts::best_model(x, ic = "aic") 2. │ └─x %>% filter_(crt) 3. └─dplyr::filter_(., crt) 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: simts Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignettes.Rmd’ using rmarkdown warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution Quitting from vignettes.Rmd:294-296 [unnamed-chunk-24] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─simts::select(AR(15), sunspot) 2. │ └─simts::best_model(out, ic = criterion) 3. │ └─x %>% filter_(crt) 4. └─dplyr::filter_(., crt) 5. └─dplyr:::lazy_defunct("filter") 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'vignettes.Rmd' failed with diagnostics: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘vignettes.Rmd’ SUMMARY: processing the following file failed: ‘vignettes.Rmd’ Error: Vignette re-building failed. Execution halted Package: soc.ca Check: R code for possible problems New result: NOTE mca.triads : get.sup: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: SomaDataIO Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [39s/42s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(SomaDataIO) ═══════════════════════════════════════════════════════════════════════ Legal ══ SomaDataIO™ Copyright © 2025 Standard BioTools, Inc. The `SomaDataIO` package is licensed under the MIT license (`LICENSE.md`) and is intended solely for research use only ("RUO") purposes. The code contained herein may *not* be used for diagnostic, clinical, therapeutic, or other commercial purposes. Further, "SomaDataIO" and "SomaLogic" are trademarks owned by Standard BioTools, Inc. No license is hereby granted to these trademarks other than for purposes of identifying the origin or source of the Software. The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDER(S) BE LIABLE FOR ANY CLAIM, DAMAGES, WHETHER DIRECT OR INDIRECT, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ════════════════════════════════════════════════════════════════════════════════ Attaching package: 'SomaDataIO' The following object is masked from 'package:stats': filter > > test_check("SomaDataIO") v ADAT passed all checks and traps. v ADAT passed all checks and traps. v ADAT passed all checks and traps. v ADAT passed all checks and traps. Saving _problems/test-dplyr-verbs-135.R x The object is not a `soma_adat` class object: "data.frame" x Header.Meta and/or Col.Meta missing from attributes. x Header.Meta and/or Col.Meta missing from attributes. x Header.Meta is missing: "HEADER", "COL_DATA", and "ROW_DATA" x Col.Meta is missing: "SeqId", "Dilution", "Target", and "Units" x Col.Meta is not a tibble! -> "list" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpV5Q6Ff/write-2093633a41f16d.adat" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpV5Q6Ff/write-2093632f2e13cc.adat" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpV5Q6Ff/write-209363bceea07.txt" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpV5Q6Ff/write-20936316529dab.adat" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpV5Q6Ff/write-209363144b85bc.adat" [ FAIL 1 | WARN 0 | SKIP 35 | PASS 993 ] ══ Skipped tests (35) ══════════════════════════════════════════════════════════ • On CRAN (34): 'test-S3-median.R:4:1', 'test-S3-merge.R:3:1', 'test-S3-print.R:11:1', 'test-S3-print.R:16:1', 'test-S3-print.R:21:1', 'test-S3-print.R:26:1', 'test-S3-print.R:32:1', 'test-S3-summary.R:49:1', 'test-diffAdats.R:6:1', 'test-diffAdats.R:10:1', 'test-diffAdats.R:15:1', 'test-diffAdats.R:20:1', 'test-diffAdats.R:27:1', 'test-diffAdats.R:34:1', 'test-getAnalytes.R:23:3', 'test-getTargetNames.R:11:1', 'test-groupGenerics.R:77:1', 'test-groupGenerics.R:182:1', 'test-is-intact-attr.R:44:1', 'test-loadAdatsAsList.R:21:1', 'test-loadAdatsAsList.R:27:1', 'test-loadAdatsAsList.R:57:1', 'test-parseCheck.R:8:1', 'test-parseHeader.R:7:1', 'test-preProcessAdat.R:2:1', 'test-preProcessAdat.R:22:1', 'test-read-adat.R:12:1', 'test-read-adat.R:38:1', 'test-scaleAnalytes.R:65:1', 'test-scaleAnalytes.R:71:1', 'test-utils-read-adat.R:9:1', 'test-utils-read-adat.R:151:1', 'test-utils-release.R:3:1', 'test-utils-release.R:16:1' • On Linux (1): 'test-preProcessAdat.R:7:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-dplyr-verbs.R:135:3'): `left_join()` method produces expected output ── Expected `names(attributes(new))` to equal `names(attributes(data))`. Differences: actual | expected [1] "names" | "names" [1] [2] "row.names" - "class" [2] [3] "class" - "row.names" [3] [4] "Header.Meta" | "Header.Meta" [4] [5] "Col.Meta" | "Col.Meta" [5] [6] "file_specs" | "file_specs" [6] [ FAIL 1 | WARN 0 | SKIP 35 | PASS 993 ] Deleting unused snapshots: 'preProcessAdat/preProcessAdat_qc_plot_Age.png' Error: ! Test failures. Execution halted Package: srvyr Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'srvyr-se-deprecated.Rd': ‘[dplyr]{se-deprecated}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: ssimparser Check: examples New result: ERROR Running examples in ‘ssimparser-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: load_ssim > ### Title: load_ssim > ### Aliases: load_ssim > > ### ** Examples > > # Get a sample as a character vector > sample_ssim_string <- ssimparser::get_ssim_sample(datefrom = as.Date("2020-11-01"), + dateto = as.Date("2020-12-01"), + season = "W20", + creadate = as.Date("2020-12-02")) > > # Write sample to temp dir > sample_ssim_file <- tempfile() > write(sample_ssim_string, sample_ssim_file, append = FALSE) > > # Load sample, expand schedules to flights and display the traffic > # by month and departure airport ICAO > ssimparser::load_ssim(ssim_file = sample_ssim_file, + expand_sched = TRUE) %>% + dplyr::group_by(format(flight.flight_date,"%Y-%m"), adep_icao) %>% + dplyr::summarise(n=dplyr::n()) [1] "File to load has 17 rows" [1] "data frame has 17 rows" Error in `dplyr::summarise()`: ℹ In argument: `n_flight = seq(1:(diff_days + 1))`. ℹ In group 1: `type2.timemode = "L"`, `type2.iata_airline = "AF"`, `type2.blank1 = " "`, `type2.season = "W20"`, `type2.blank2 = " "`, `type2.valid_from = "01NOV20"`, `type2.valid_to = "01DEC20"`, `type2.creation_date = "02DEC20"`, `type2.title_of_data = "SSIM EXAMPLE SCHEDULE "`, `type2.release_date = "02DEC20"`, `type2.schedule_status = "C"`, `type2.creator_reference = "KENNY"`, `type2.duplicate_airline_designator = ""`, `type2.general_information = "TEST AIRLINE"`, `type2.inflight_service_information = "1/8/13/18"`, `type2.electronic_ticketing_information = "ET"`, `type2.creation_time = "1800"`, `type2.record_serial_number = 2`, …, `type3.period_from_utc = 2020-11-01`, `type3.period_to_utc = 2020-11-16`. Caused by error: ! `n_flight` must be size 1, not 16. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─... %>% dplyr::summarise(n = dplyr::n()) 2. ├─dplyr::summarise(., n = dplyr::n()) 3. ├─dplyr::group_by(., format(flight.flight_date, "%Y-%m"), adep_icao) 4. ├─ssimparser::load_ssim(ssim_file = sample_ssim_file, expand_sched = TRUE) 5. │ └─... %>% dplyr::select(-n_flight, day_of_operation) 6. ├─dplyr::select(., -n_flight, day_of_operation) 7. ├─dplyr::ungroup(.) 8. ├─dplyr::filter(...) 9. ├─dplyr::mutate(., day_of_operation = as.character(get_day_of_week(as.Date(flight.flight_date)))) 10. ├─dplyr::rowwise(.) 11. ├─dplyr::mutate(...) 12. ├─dplyr::filter(...) 13. ├─dplyr::ungroup(.) 14. ├─dplyr::summarise(., n_flight = seq(1:(diff_days + 1))) 15. ├─dplyr:::summarise.grouped_df(., n_flight = seq(1:(diff_days + 1))) 16. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 17. │ └─base::withCallingHandlers(...) 18. ├─dplyr:::dplyr_internal_error(...) 19. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 20. │ └─rlang:::signal_abort(cnd, .file) 21. │ └─base::signalCondition(cnd) 22. └─dplyr (local) ``(``) 23. └─dplyr (local) handler(cnd) 24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Package: stabiliser Check: R code for possible problems New result: NOTE perm_model: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: statsExpressions Check: tests New result: ERROR Running ‘testthat.R’ [286s/166s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(patrick) > library(statsExpressions) > > test_check("statsExpressions") Starting 2 test processes. > test-oneway-anova-bayes.R: Multiple `BFBayesFactor` models detected - posteriors are extracted from > test-oneway-anova-bayes.R: the first numerator model. > test-oneway-anova-bayes.R: See help("get_parameters", package = "insight"). > test-oneway-anova-bayes.R: Multiple `BFBayesFactor` models detected - posteriors are extracted from > test-oneway-anova-bayes.R: the first numerator model. > test-oneway-anova-bayes.R: See help("get_parameters", package = "insight"). > test-oneway-anova-bayes.R: Multiple `BFBayesFactor` models detected - posteriors are extracted from > test-oneway-anova-bayes.R: the first numerator model. > test-oneway-anova-bayes.R: See help("get_parameters > test-oneway-anova-bayes.R: ", package = "insight"). > test-oneway-anova-bayes.R: Multiple `BFBayesFactor` models detected - posteriors are extracted from > test-oneway-anova-bayes.R: the first numerator model. > test-oneway-anova-bayes.R: See help("get_parameters", package = "insight"). Saving _problems/test-oneway-anova-bayes-18.R [ FAIL 1 | WARN 4 | SKIP 64 | PASS 28 ] ══ Skipped tests (64) ══════════════════════════════════════════════════════════ • On CRAN (63): 'test-centrality-description.R:1:1', 'test-centrality-description.R:49:1', 'test-corr-test.R:3:1', 'test-corr-test.R:39:1', 'test-corr-test.R:74:1', 'test-corr-test.R:110:1', 'test-long-to-wide-converter.R:3:1', 'test-long-to-wide-converter.R:53:1', 'test-contingency-table.R:1:1', 'test-contingency-table.R:49:1', 'test-contingency-table.R:108:1', 'test-contingency-table.R:156:1', 'test-contingency-table.R:184:1', 'test-meta-random-parametric.R:1:1', 'test-meta-random-robust.R:1:1', 'test-meta-random-bayes.R:1:1', 'test-one-two-sample-dataframes.R:1:1', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-one-sample.R:10:3', 'test-oneway-anova-nonparametric.R:5:1', 'test-oneway-anova-nonparametric.R:41:1', 'test-oneway-anova-parametric.R:1:1', 'test-oneway-anova-parametric.R:35:1', 'test-oneway-anova-parametric.R:53:1', 'test-oneway-anova-bayes.R:39:1', 'test-pairwise-comparisons.R:3:1', 'test-pairwise-comparisons.R:98:1', 'test-pairwise-comparisons.R:131:1', 'test-pairwise-comparisons.R:152:1', 'test-pairwise-comparisons.R:218:1', 'test-pairwise-comparisons.R:318:1', 'test-tidy-model-expressions.R:1:1', 'test-tidy-model-expressions.R:33:1', 'test-tidy-model-expressions.R:57:1', 'test-tidy-model-expressions.R:78:1', 'test-two-sample-bayes.R:1:1', 'test-two-sample-bayes.R:18:1', 'test-two-sample-nonparametric.R:1:1', 'test-two-sample-nonparametric.R:22:1', 'test-two-sample-parametric.R:1:1', 'test-two-sample-parametric.R:23:1', 'test-two-sample-parametric.R:45:1', 'test-two-sample-parametric.R:66:1', 'test-two-sample-robust.R:3:1', 'test-two-sample-robust.R:25:1', 'test-two-sample-robust.R:45:1', 'test-two-sample-robust.R:68:1', 'test-oneway-anova-robust.R:1:1', 'test-oneway-anova-robust.R:40:1' • On Linux (1): 'test-centrality-description.R:27:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-oneway-anova-bayes.R:13:5'): bayesian (between-subjects - anova) ── Error in `data$method[[1L]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-oneway-anova-bayes.R:13:5 2. │ └─base::withCallingHandlers(...) 3. └─statsExpressions::oneway_anova(...) 4. └─statsExpressions::add_expression_col(...) 5. └─base::grepl("contingency", data$method[[1L]], fixed = TRUE) 6. └─base::is.factor(x) [ FAIL 1 | WARN 4 | SKIP 64 | PASS 28 ] Error: ! Test failures. Execution halted Package: StratifiedMedicine Check: R code for possible problems New result: NOTE plot_ple: no visible binding for global variable ‘id’ plot_tree: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: survivoR Check: R code for possible problems New result: NOTE apply_edits: no visible binding for global variable ‘id’ conf_app_server: no visible binding for global variable ‘id’ get_confessional_timing: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: survminer Check: examples New result: ERROR Running examples in ‘survminer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: surv_fit > ### Title: Create Survival Curves > ### Aliases: surv_fit > > ### ** Examples > > > library("survival") Attaching package: ‘survival’ The following object is masked from ‘package:survminer’: myeloma > library("magrittr") > > # Case 1: One formula and One data set > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > fit <- surv_fit(Surv(time, status) ~ sex, + data = colon) > surv_pvalue(fit) variable pval method pval.txt 1 sex 0.6107936 Log-rank p = 0.61 > > > # Case 2: List of formulas and One data set. > # - Different formulas are applied to the same data set > # - Returns a (named) list of survfit objects > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > # Create a named list of formulas > formulas <- list( + sex = Surv(time, status) ~ sex, + rx = Surv(time, status) ~ rx + ) > > # Fit survival curves for each formula > fit <- surv_fit(formulas, data = colon) > surv_pvalue(fit) $`colon::sex` variable pval method pval.txt 1 sex 0.6107936 Log-rank p = 0.61 $`colon::rx` variable pval method pval.txt 1 rx 4.990735e-08 Log-rank p < 0.0001 > > # Case 3: One formula and List of data sets > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > fit <- surv_fit(Surv(time, status) ~ sex, + data = list(colon, lung)) > surv_pvalue(fit) $`colon::sex` variable pval method pval.txt 1 sex 0.6107936 Log-rank p = 0.61 $`lung::sex` variable pval method pval.txt 1 sex 0.001311165 Log-rank p = 0.0013 > > > # Case 4: List of formulas and List of data sets > # - Each formula is applied to each of the data in the data list > # - argument: match.fd = FALSE > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > > # Create two data sets > set.seed(123) > colon1 <- dplyr::sample_frac(colon, 1/2) > set.seed(1234) > colon2 <- dplyr::sample_frac(colon, 1/2) > > # Create a named list of formulas > formula.list <- list( + sex = Surv(time, status) ~ sex, + adhere = Surv(time, status) ~ adhere, + rx = Surv(time, status) ~ rx + ) > > # Fit survival curves > fit <- surv_fit(formula.list, data = list(colon1, colon2), + match.fd = FALSE) Error: ! `combine()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `vctrs::vec_c()` instead. Backtrace: ▆ 1. ├─survminer::surv_fit(...) 2. │ └─purrr::map(formula, .map_each, data) %>% dplyr::combine() 3. └─dplyr::combine(.) 4. └─lifecycle::deprecate_stop("1.0.0", "combine()", "vctrs::vec_c()") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed ggsurvplot 6.386 0 6.490 ggsurvplot_group_by 6.174 0 6.174 Package: telraamStats Check: examples New result: ERROR Running examples in ‘telraamStats-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: enrich_special_days > ### Title: Enrich traffic data with french vacation and public holidays > ### Aliases: enrich_special_days > ### Keywords: internal > > ### ** Examples > > df <- data.frame('day' = as.Date(c("2022-02-18","2022-01-01")), + 'date' = c('2022-02-18 12:00:00 CET','2022-01-01 12:00:00 CET')) > enrich_special_days(df) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [data.education.gouv.fr]: Connection timed out after 10001 milliseconds Calls: enrich_special_days ... request_fetch.write_memory -> -> raise_libcurl_error Execution halted Package: Tendril Check: examples New result: ERROR Running examples in ‘Tendril-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Tendril > ### Title: Tendril > ### Aliases: Tendril > > ### ** Examples > > data <- Tendril(mydata = TendrilData, + rotations = Rotations, + AEfreqThreshold=9, + Tag = "Comment", + Treatments = c("placebo", "active"), + Unique.Subject.Identifier = "subjid", + Terms = "ae", + Treat = "treatment", + StartDay = "day", + SubjList = SubjList, + SubjList.subject = "subjid", + SubjList.treatment = "treatment" + ) Error: ! `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: Tendril Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘TendrilUsage.Rmd’ using rmarkdown Quitting from TendrilUsage.Rmd:28-51 [example_plot] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. --- Backtrace: ▆ 1. └─Tendril::Tendril(...) 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'TendrilUsage.Rmd' failed with diagnostics: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. --- failed re-building ‘TendrilUsage.Rmd’ SUMMARY: processing the following file failed: ‘TendrilUsage.Rmd’ Error: Vignette re-building failed. Execution halted Package: Tendril Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Tendril) > > test_check("Tendril") Saving _problems/test_plot_timeseries-21.R Saving _problems/test_tendrilData-251.R Saving _problems/test_tendrilData-337.R Saving _problems/test_tendrilData-365.R Saving _problems/test_tendrilData-395.R Saving _problems/test_tendrilData-426.R Saving _problems/test_tendrilData-458.R Saving _problems/test_tendrilData-492.R Saving _problems/test_tendrilData-522.R Saving _problems/test_tendrilPerm-25.R Saving _problems/test_tendrilPerm-137.R [ FAIL 11 | WARN 0 | SKIP 0 | PASS 12 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_plot_timeseries.R:8:5'): Creation of plot timeseries ─────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_plot_timeseries.R:7:3 2. │ └─base::withCallingHandlers(...) 3. └─Tendril::Tendril(...) at test_plot_timeseries.R:8:5 4. └─Tendril:::dataSetup(...) 5. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 6. └─dplyr:::lazy_defunct("rename", hint = FALSE) 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:238:5'): tendril_result_correct ────────────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:238:5 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:324:3'): tendril_result_correct_filter_double_events ── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:324:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:356:3'): tendril_result_no_SubjList_supplied ───── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilData.R:356:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:384:3'): tendril_result_no_SubjList_supplied_single_rotation_factor ── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilData.R:384:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:413:3'): tendril_proportional_rotation_factor ──── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:413:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:445:3'): tendril_error_event_after_dropout ─────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilData.R:445:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:478:3'): tendril_check_correct_imbalance_and_variable_rotation ── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:478:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:509:3'): tendril_check_for_presence_of_term ────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:509:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilPerm.R:14:5'): input_perm_valid ───────────────────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilPerm.R:13:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) at test_tendrilPerm.R:14:5 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilPerm.R:126:5'): output_perm_valid ─────────────────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilPerm.R:125:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) at test_tendrilPerm.R:126:5 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) [ FAIL 11 | WARN 0 | SKIP 0 | PASS 12 ] Error: ! Test failures. Execution halted Package: TextForecast Check: examples New result: ERROR Running examples in ‘TextForecast-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_collocations > ### Title: get_collocations function > ### Aliases: get_collocations > > ### ** Examples > > path_name=system.file("news",package="TextForecast") > days=c("2019-30-01","2019-31-01") > z_coll=get_collocations(corpus_dates=days[1],path_name=path_name, + ntrms=500,ngrams_number=3,min_freq=1) Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.5/master/inst/udpipe-ud-2.5-191206/english-ewt-ud-2.5-191206.udpipe to /home/hornik/tmp/scratch/RtmpusSB3Q/english-ewt-ud-2.5-191206.udpipe - This model has been trained on version 2.5 of data from https://universaldependencies.org - The model is distributed under the CC-BY-SA-NC license: https://creativecommons.org/licenses/by-nc-sa/4.0 - Visit https://github.com/jwijffels/udpipe.models.ud.2.5 for model license details. - For a list of all models and their licenses (most models you can download with this package have either a CC-BY-SA or a CC-BY-SA-NC license) read the documentation at ?udpipe_download_model. For building your own models: visit the documentation by typing vignette('udpipe-train', package = 'udpipe') trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.5/master/inst/udpipe-ud-2.5-191206/english-ewt-ud-2.5-191206.udpipe' Content type 'application/octet-stream' length 16309608 bytes (15.6 MB) ================================================== downloaded 15.6 MB Downloading finished, model stored at '/home/hornik/tmp/scratch/RtmpusSB3Q/english-ewt-ud-2.5-191206.udpipe' [1] "2019-30-01" [1] "2026-02-01 22:28:46 CET" Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. └─TextForecast::get_collocations(...) 2. └─dplyr::tbl_df(Tdm.stack) 3. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 4. └─lifecycle:::deprecate_stop0(msg) 5. └─rlang::cnd_signal(...) Execution halted Package: tidyCDISC Check: R code for possible problems New result: NOTE app_lineplot: no visible binding for global variable ‘id’ mod_indvExpPatEvents_server: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: tidycensus Check: R code for possible problems New result: NOTE get_flows: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: tidyseurat Check: tests New result: ERROR Running ‘testthat.R’ [18s/18s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(tidyseurat) Loading required package: ttservice Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t ======================================== tidyseurat version 0.8.7 If you use TIDYSEURAT in published research, please cite: Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021. This message can be suppressed by: suppressPackageStartupMessages(library(tidyseurat)) To restore the Seurat default display use options("restore_Seurat_show" = TRUE) ======================================== Attaching package: 'tidyseurat' The following object is masked from 'package:ttservice': plot_ly > > test_check("tidyseurat") Saving _problems/test-dplyr-208.R Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| [ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-dplyr.R:205:3'): add_count ───────────────────────────────────── Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and is now defunct. Backtrace: ▆ 1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(add_count(pbmc_small, groups)) 5. ├─dplyr::add_count(pbmc_small, groups) 6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups) 7. │ └─... %>% as_meta_data(x) 8. ├─tidyseurat:::as_meta_data(., x) 9. │ └─... %>% column_to_rownames(c_(seurat_object)$name) 10. ├─tibble::column_to_rownames(., c_(seurat_object)$name) 11. │ ├─base::stopifnot(is.data.frame(.data)) 12. │ └─base::is.data.frame(.data) 13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude) 14. │ └─rlang::is_logical(.predicate) 15. ├─colnames(.) %in% col_to_exclude 16. ├─base::colnames(.) 17. │ └─base::is.data.frame(x) 18. ├─dplyr::add_count(...) 19. └─dplyr:::add_count.data.frame(...) 20. └─dplyr:::add_count_impl(...) 21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call) 22. └─lifecycle:::deprecate_stop0(msg) 23. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ] Error: ! Test failures. Execution halted Package: timelineS Check: examples New result: ERROR Running examples in ‘timelineS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: durPlot > ### Title: Graphs and Summary for Date Durations > ### Aliases: durPlot > > ### ** Examples > > durPlot(life_exp, start = "Birth", end = "Death", group = "Country", + timeunit = "years", facet = TRUE, binwidth = 3, alpha = 0.7, title = TRUE) Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. ℹ The deprecated feature was likely used in the timelineS package. Please report the issue at . Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─timelineS::durPlot(...) 2. │ └─df %>% group_by_(as.name(group)) 3. └─dplyr::group_by_(., as.name(group)) 4. └─dplyr:::lazy_defunct("group_by") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: traineR Check: examples New result: ERROR Running examples in ‘traineR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: categorical.predictive.power > ### Title: categorical.predictive.power > ### Aliases: categorical.predictive.power > > ### ** Examples > > > cars <- datasets::mtcars > cars$cyl <- as.factor(cars$cyl) > cars$vs <- as.factor(cars$vs) > categorical.predictive.power(cars,"vs","cyl") Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. └─traineR::categorical.predictive.power(cars, "vs", "cyl") 2. ├─base::suppressWarnings(...) 3. │ └─base::withCallingHandlers(...) 4. ├─dplyr::summarise(...) 5. └─dplyr::group_by_(data, variable.to.compare, predict.variable) 6. └─dplyr:::lazy_defunct("group_by") 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) Execution halted Package: tvgeom Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘introduction.Rmd’ using rmarkdown Quitting from introduction.Rmd:153-155 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─global plot_param(d_phi, d_y, "k", "L_max == min(L_max)") 2. │ └─... %>% ... 3. └─dplyr::filter_(., subset) 4. └─dplyr:::lazy_defunct("filter") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'introduction.Rmd' failed with diagnostics: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `filter()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘introduction.Rmd’ SUMMARY: processing the following file failed: ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: twfeivdecomp Check: R code for possible problems New result: NOTE calculate_mean_linear_projection: no visible binding for global variable ‘id’ calculate_within_between_terms: no visible binding for global variable ‘id’ create_cohort: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: TwoArmSurvSim Check: R code for possible problems New result: NOTE randomize_trt: no visible binding for global variable ‘id’ randomize_trt2: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: ulex Check: R code for possible problems New result: NOTE locate_event_i: no visible binding for global variable ‘location’ Undefined global functions or variables: location Package: useful Check: examples New result: ERROR Running examples in ‘useful-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: moveToFront > ### Title: moveToFront > ### Aliases: moveToFront moveToBack > > ### ** Examples > > theDF <- data.frame(A=1:10, B=11:20, C=1:10, D=11:20) > moveToFront(theDF, c('B', 'C')) Error: ! `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─useful::moveToFront(theDF, c("B", "C")) 2. │ └─data %>% select_(.dots = colOrder) 3. └─dplyr::select_(., .dots = colOrder) 4. └─dplyr:::lazy_defunct("select", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: useful Check: tests New result: ERROR Running ‘testthat.R’ [15s/18s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(useful) Loading required package: ggplot2 > > test_check("useful") Error in detach("package:coefplot", unload = TRUE) : invalid 'name' argument Saving _problems/test-move-cols-37.R Saving _problems/test-move-cols-46.R Saving _problems/test-move-cols-55.R Saving _problems/test-unique-7.R [ FAIL 4 | WARN 7 | SKIP 2 | PASS 721 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-load-packages.R:11:5', 'test-load-packages.R:18:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-move-cols.r:37:5'): cols to front/back returns data.frame ────── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_is(moveToFront(theDF, c("B", "C")), "data.frame") at test-move-cols.r:37:5 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─useful::moveToFront(theDF, c("B", "C")) 5. │ └─data %>% select_(.dots = colOrder) 6. └─dplyr::select_(., .dots = colOrder) 7. └─dplyr:::lazy_defunct("select", hint = FALSE) 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) ── Error ('test-move-cols.r:46:5'): cols to front/back returns the right dimension ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-move-cols.r:46:5 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─useful::moveToFront(theDF, c("B", "C")) 5. │ └─data %>% select_(.dots = colOrder) 6. └─dplyr::select_(., .dots = colOrder) 7. └─dplyr:::lazy_defunct("select", hint = FALSE) 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) ── Error ('test-move-cols.r:55:5'): cols to front/back returns the right names ── Error: `select_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `select()` instead. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-move-cols.r:55:5 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─useful::moveToFront(theDF, c("B", "C")) 5. │ └─data %>% select_(.dots = colOrder) 6. └─dplyr::select_(., .dots = colOrder) 7. └─dplyr:::lazy_defunct("select", hint = FALSE) 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) ── Error ('test-unique.R:7:1'): (code run outside of `test_that()`) ──────────── Error: `as.tbl()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. └─dplyr::as.tbl(...) at test-unique.R:7:1 2. └─lifecycle::deprecate_stop("1.0.0", "as.tbl()", "tibble::as_tibble()") 3. └─lifecycle:::deprecate_stop0(msg) 4. └─rlang::cnd_signal(...) [ FAIL 4 | WARN 7 | SKIP 2 | PASS 721 ] Error: ! Test failures. Execution halted Package: viafr Check: R code for possible problems New result: NOTE get_source_ids: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: vpc Check: examples New result: ERROR Running examples in ‘vpc-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: vpc_tte > ### Title: VPC function for time-to-event (survival) data > ### Aliases: vpc_tte > > ### ** Examples > > ## See vpc-docs.ronkeizer.com for more documentation and examples. > > ## Example for repeated) time-to-event data > ## with NONMEM-like data (e.g. simulated using a dense grid) > > data(rtte_obs_nm) > data(rtte_sim_nm) > > # treat RTTE as TTE, no stratification > vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,], + obs = rtte_obs_nm, + rtte = FALSE, + sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t")) Initializing. Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─vpc::vpc_tte(...) 2. │ └─... %>% dplyr::filter(!duplicated(id)) 3. ├─dplyr::filter(., !duplicated(id)) 4. ├─dplyr::filter(., dv == 1 | last_obs == 1) 5. ├─dplyr::mutate(...) 6. └─dplyr::group_by_(., "id") 7. └─dplyr:::lazy_defunct("group_by") 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) Execution halted Package: vpc Check: tests New result: ERROR Running ‘test-add_sim_index_number.R’ [10s/10s] Running ‘test-filter_dv.R’ [1s/1s] Running ‘test-labeller.R’ [6s/6s] Running ‘test-scales.R’ [4s/4s] Running ‘test-softwaretype.R’ [1s/1s] Running ‘test-strat-col-detection.R’ [1s/1s] Running ‘test-vpc.R’ [4s/5s] Running ‘test-vpc_cat.R’ [3s/3s] Running ‘test-vpc_cens.R’ [5s/5s] Running ‘test-vpc_tte.R’ [2s/2s] Running the tests in ‘tests/test-add_sim_index_number.R’ failed. Complete output: > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(vpc) > library(testit) > Sys.setenv("R_TESTS" = "") > > ## Load the theophylline PK dataset > obs <- Theoph > colnames(obs) <- c("id", "wt", "dose", "time", "dv") > obs <- obs %>% + dplyr::group_by(id) %>% + mutate(sex = round(runif(1))) # randomly assign a "sex" covariate > sim <- sim_data(obs, # the design of the dataset + model = function(x) { # the model + vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt) + }, + error = list(additive = 0.1), + theta = c(2.774, 0.0718, .0361), # parameter values + omega_mat = c(0.08854, # specified as lower triangle by default; + 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv. + 0.008069, 0.008639, 0.02862), + par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas + n = 500) Error: ! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─vpc::sim_data(...) 2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time") 3. └─dplyr::arrange_(., "sim", "id", "time") 4. └─dplyr:::lazy_defunct("arrange") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Running the tests in ‘tests/test-vpc_tte.R’ failed. Complete output: > library(vpc) > library(testit) > Sys.setenv("R_TESTS" = "") > > ## Test for bug AR 20171025 column name simulation dataset > test <- vpc::rtte_sim_nm[1:200000,] > test$bla <- test$t > test$t <- NULL > obj <- vpc_tte(sim = test, # stratified for covariate and study arm + obs = vpc::rtte_obs_nm, + rtte = FALSE, + sim_cols = list(dv = "dv", idv = "bla"), + obs_cols = list(idv = "t"), + labeller = ggplot2::label_both) Initializing. Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─vpc::vpc_tte(...) 2. │ └─... %>% dplyr::filter(!duplicated(id)) 3. ├─dplyr::filter(., !duplicated(id)) 4. ├─dplyr::filter(., dv == 1 | last_obs == 1) 5. ├─dplyr::mutate(...) 6. └─dplyr::group_by_(., "id") 7. └─dplyr:::lazy_defunct("group_by") 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) Execution halted Package: wakefield Check: examples New result: ERROR Running examples in ‘wakefield-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: as_integer > ### Title: Convert a Factor Data Frame to Integer > ### Aliases: as_integer > ### Keywords: integer numeric > > ### ** Examples > > as_integer(r_series(likert_7, 5, 10)) Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace: ▆ 1. ├─wakefield::as_integer(r_series(likert_7, 5, 10)) 2. │ └─base::lapply(x, fun) 3. └─wakefield::r_series(likert_7, 5, 10) 4. ├─wakefield::seriesname(dplyr::tbl_df(as.data.frame(out)), attributes(out[[1]])[["varname"]]) 5. └─dplyr::tbl_df(as.data.frame(out)) 6. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()") 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: xlr Check: tests New result: ERROR Running ‘testthat.R’ [43s/43s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(xlr) > > test_check("xlr") Saving _problems/test-build_multiple_response_table-22.R Saving _problems/test-build_multiple_response_table-43.R Saving _problems/test-build_multiple_response_table-66.R Saving _problems/test-build_multiple_response_table-90.R Saving _problems/test-build_multiple_response_table-328.R Saving _problems/test-build_multiple_response_table-352.R Saving _problems/test-build_multiple_response_table-383.R Saving _problems/test-build_multiple_response_table-507.R Saving _problems/test-build_multiple_response_table-530.R Saving _problems/test-build_multiple_response_table-560.R Saving _problems/test-build_multiple_response_table-650.R Saving _problems/test-build_multiple_response_table-672.R Saving _problems/test-build_multiple_response_table-696.R Saving _problems/test-build_multiple_response_table-723.R Saving _problems/test-build_multiple_response_table-742.R Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union [ FAIL 15 | WARN 0 | SKIP 100 | PASS 655 ] ══ Skipped tests (100) ═════════════════════════════════════════════════════════ • On CRAN (100): 'test-build_multiple_response_table.R:183:1', 'test-build_multiple_response_table.R:187:1', 'test-build_multiple_response_table.R:193:1', 'test-build_multiple_response_table.R:199:1', 'test-build_multiple_response_table.R:205:1', 'test-build_multiple_response_table.R:210:1', 'test-build_multiple_response_table.R:236:1', 'test-build_multiple_response_table.R:270:1', 'test-build_multiple_response_table.R:277:1', 'test-build_multiple_response_table.R:290:1', 'test-build_multiple_response_table.R:299:1', 'test-build_multiple_response_table.R:746:1', 'test-build_question_block_table.R:1:1', 'test-build_question_block_table.R:6:1', 'test-build_question_block_table.R:12:1', 'test-build_question_block_table.R:17:1', 'test-build_question_block_table.R:32:1', 'test-build_question_block_table.R:41:1', 'test-build_question_block_table.R:253:1', 'test-build_table.R:1:1', 'test-build_table.R:9:1', 'test-build_table.R:85:1', 'test-create_table_of_contents.R:17:1', 'test-create_table_of_contents.R:29:1', 'test-create_table_of_contents.R:40:1', 'test-create_table_of_contents.R:51:1', 'test-create_table_of_contents.R:63:1', 'test-create_table_of_contents.R:75:1', 'test-create_table_of_contents.R:155:3', 'test-error_utils.R:1:1', 'test-make_wider.R:1:1', 'test-make_wider.R:9:1', 'test-make_wider.R:23:1', 'test-make_wider.R:85:1', 'test-make_wider.R:122:1', 'test-table_utils.R:44:1', 'test-table_utils.R:55:1', 'test-table_utils.R:89:1', 'test-table_utils.R:111:1', 'test-table_utils.R:133:1', 'test-table_utils.R:155:1', 'test-table_utils.R:178:1', 'test-table_utils.R:201:1', 'test-write_xlsx.R:16:1', 'test-write_xlsx.R:32:1', 'test-write_xlsx.R:54:1', 'test-write_xlsx.R:76:1', 'test-xlr_format.R:3:1', 'test-xlr_format.R:217:1', 'test-xlr_format.R:241:1', 'test-xlr_format.R:254:1', 'test-xlr_integer.R:60:1', 'test-xlr_integer.R:142:1', 'test-xlr_integer.R:186:1', 'test-xlr_n_percent.R:44:1', 'test-xlr_n_percent.R:95:1', 'test-xlr_n_percent.R:100:1', 'test-xlr_numeric.R:73:1', 'test-xlr_numeric.R:80:1', 'test-xlr_numeric.R:157:1', 'test-xlr_numeric.R:162:1', 'test-xlr_percent.R:95:1', 'test-xlr_percent.R:227:1', 'test-xlr_percent.R:232:1', 'test-xlr_table.R:45:1', 'test-xlr_to_workbook.R:31:1', 'test-xlr_to_workbook.R:39:1', 'test-xlr_to_workbook.R:64:1', 'test-xlr_to_workbook.R:104:1', 'test-xlr_to_workbook.R:210:3', 'test-xlr_to_workbook.R:454:3', 'test-xlr_to_workbook.R:508:3', 'test-xlr_to_workbook.R:544:3', 'test-xlr_to_workbook.R:555:1', 'test-xlr_to_workbook.R:595:3', 'test-xlr_to_workbook.R:632:3', 'test-xlr_to_workbook.R:700:3', 'test-xlr_to_workbook.R:709:1', 'test-xlr_to_workbook.R:719:1', 'test-xlr_to_workbook.R:768:3', 'test-xlr_to_workbook.R:777:1', 'test-xlr_to_workbook.R:785:1', 'test-xlr_to_workbook.R:796:1', 'test-xlr_to_workbook.R:804:1', 'test-xlr_to_workbook.R:811:1', 'test-xlr_to_workbook.R:816:1', 'test-xlr_to_workbook.R:821:1', 'test-xlr_to_workbook.R:826:1', 'test-xlr_to_workbook.R:834:1', 'test-xlr_to_workbook.R:841:1', 'test-xlr_to_workbook.R:846:1', 'test-xlr_to_workbook.R:852:1', 'test-xlr_to_workbook.R:858:1', 'test-xlr_to_workbook.R:884:3', 'test-xlr_to_workbook.R:929:3', 'test-xlr_to_workbook.R:964:3', 'test-xlr_to_workbook.R:999:3', 'test-xlr_vector.R:68:1', 'test-xlr_vector.R:79:1', 'test-xlr_vector.R:92:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-build_multiple_response_table.R:22:3'): build_multiple_response_table() works for the simplest case ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" `actual$N_group`: `expected$N_group`: "6" "6" "6" `actual$Percent`: `expected$Percent`: "50%" "67%" "83%" ── Failure ('test-build_multiple_response_table.R:43:3'): build_multiple_response_table() works with question labels ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" `actual$N_group`: `expected$N_group`: "6" "6" "6" `actual$Percent`: `expected$Percent`: "50%" "67%" "83%" ── Failure ('test-build_multiple_response_table.R:66:3'): build_multiple_response_table() works when we add one grouping variable ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 5 6 7 8 `actual$col_1`: `expected$col_1`: "a" "a" "a" "b" "b" "c" "c" "c" `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "2" "1" "2" "2" "2" "1" "1" "1" `actual$N_group`: `expected$N_group`: "2" "2" "2" "2" "2" "2" "2" "2" `actual$Percent`: `expected$Percent`: "100%" "50%" "100%" "100%" "100%" "50%" "50%" "50%" ── Failure ('test-build_multiple_response_table.R:90:3'): build_multiple_response_table() works when we add two grouping variables ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 5 6 7 8 9 10 `actual$col_1`: `expected$col_1`: "a" "a" "a" "b" "b" "b" "b" "c" "c" "c" `actual$col_2`: `expected$col_2`: "d" "d" "d" "d" "d" "e" "e" "e" "e" "e" `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "2" "1" "2" "1" "1" "1" "1" "1" "1" "1" `actual$N_group`: `expected$N_group`: "2" "2" "2" "1" "1" "1" "1" "2" "2" "2" actual$Percent | expected$Percent - "100%" [1] - "50%" [2] - "100%" [3] - "100%" [4] - "100%" [5] - "100%" [6] - "100%" [7] - "50%" [8] - "50%" [9] - "50%" [10] ── Failure ('test-build_multiple_response_table.R:328:3'): build_multiple_response_table() works for a simple NA case ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" "1" `actual$N_group`: `expected$N_group`: "7" "7" "7" "7" `actual$Percent`: `expected$Percent`: "43%" "57%" "71%" "14%" ── Failure ('test-build_multiple_response_table.R:352:3'): build_multiple_response_table() works for NA case and a column group ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 5 6 7 8 9 `actual$col_1`: `expected$col_1`: "a" "a" "a" "b" "b" "c" "c" "c" "c" `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "2" "1" "2" "2" "2" "1" "1" "1" "1" `actual$N_group`: `expected$N_group`: "2" "2" "2" "2" "2" "3" "3" "3" "3" `actual$Percent`: `expected$Percent`: "100%" "50%" "100%" "100%" "100%" "33%" "33%" "33%" "33%" ── Failure ('test-build_multiple_response_table.R:383:3'): build_multiple_response_table() works for NA for a group and multiple response column ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: and 1 more... `attr(expected, 'row.names')`: 1 2 3 4 5 6 7 8 9 10 ... actual$col_1 | expected$col_1 - "a " [1] - "a " [2] - "b " [3] - "b " [4] - "c " [5] - "c " [6] - "c " [7] - "c " [8] - "NA" [9] - "NA" [10] ... ... ... and 1 more ... `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: and 1 more... `expected$N`: "1" "1" "2" "2" "1" "1" "1" "1" "1" "1" ... `actual$N_group`: and 1 more... `expected$N_group`: "1" "1" "2" "2" "3" "3" "3" "3" "1" "1" ... actual$Percent | expected$Percent - "100%" [1] - "100%" [2] - "100%" [3] - "100%" [4] - "33%" [5] - "33%" [6] - "33%" [7] - "33%" [8] - "100%" [9] - "100%" [10] ... ... ... and 1 more ... ── Failure ('test-build_multiple_response_table.R:507:3'): build_mtable works with weights in the simplest case ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "0.7" "0.7" "0.9" `actual$N_group`: `expected$N_group`: "1.2" "1.2" "1.2" `actual$Percent`: `expected$Percent`: "58%" "58%" "75%" ── Failure ('test-build_multiple_response_table.R:530:3'): build_mtable works with weights in the simplest case and NA ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "0.7" "0.7" "0.9" "0.4" `actual$N_group`: `expected$N_group`: "1.6" "1.6" "1.6" "1.6" `actual$Percent`: `expected$Percent`: "44%" "44%" "56%" "25%" ── Failure ('test-build_multiple_response_table.R:560:3'): build_mtable works with weights, one multiple response col, and cut column ── Expected `func_output` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 5 6 7 8 `actual$col_1`: `expected$col_1`: "a" "a" "a" "b" "b" "c" "c" "c" `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "0.4" "0.2" "0.4" "0.2" "0.2" "0.3" "0.3" "0.3" `actual$N_group`: `expected$N_group`: "0.4" "0.4" "0.4" "0.2" "0.2" "0.6" "0.6" "0.6" `actual$Percent`: `expected$Percent`: "100%" "50%" "100%" "100%" "100%" "50%" "50%" "50%" ── Failure ('test-build_multiple_response_table.R:650:3'): build_mtable works when you specify exclude_codes for 0 ── Expected `out` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" `actual$N_group`: `expected$N_group`: "6" "6" "6" `actual$Percent`: `expected$Percent`: "50%" "67%" "83%" ── Failure ('test-build_multiple_response_table.R:672:3'): build_mtable works when you specify exclude_codes for 0, with NA value ── Expected `out` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" "1" `actual$N_group`: `expected$N_group`: "7" "7" "7" "7" `actual$Percent`: `expected$Percent`: "43%" "57%" "71%" "14%" ── Failure ('test-build_multiple_response_table.R:696:3'): build_mtable works when you specify exclude_codes for a character value ── Expected `out` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" "1" `actual$N_group`: `expected$N_group`: "7" "7" "7" "7" `actual$Percent`: `expected$Percent`: "43%" "57%" "71%" "14%" ── Failure ('test-build_multiple_response_table.R:723:3'): build_mtable allows you to specify the value for seen but answered, and that this value is always LAST in the the table ── Expected `out` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "3" "4" "5" "1" `actual$N_group`: `expected$N_group`: "7" "7" "7" "7" `actual$Percent`: `expected$Percent`: "43%" "57%" "71%" "14%" ── Failure ('test-build_multiple_response_table.R:742:3'): build_mtable allows you to specify the value for seen but answered, and that this value is always LAST in the the table ── Expected `out` to equal `expected_output`. Differences: `attr(actual, 'row.names')`: `attr(expected, 'row.names')`: 1 2 3 4 5 6 7 `actual$col_1`: `expected$col_1`: "a" "a" "a" "a" "c" "c" "c" `actual$enjoy_fruit` is an S3 object of class , a logical vector `expected$enjoy_fruit` is an S3 object of class , a character vector `actual$N`: `expected$N`: "1" "1" "1" "1" "2" "3" "4" `actual$N_group`: `expected$N_group`: "3" "3" "3" "3" "4" "4" "4" `actual$Percent`: `expected$Percent`: "33%" "33%" "33%" "33%" "50%" "75%" "100%" [ FAIL 15 | WARN 0 | SKIP 100 | PASS 655 ] Error: ! Test failures. Execution halted Package: ypssc Check: R code for possible problems New result: NOTE calculationAlphaHelix: no visible binding for global variable ‘id’ calculationBetaSheet: no visible binding for global variable ‘id’ calculationChain: no visible binding for global variable ‘id’ Undefined global functions or variables: id Package: ZIBR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘zibr.Rmd’ using rmarkdown Quitting from zibr.Rmd:169-286 [unnamed-chunk-11] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `add_rownames()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::rownames_to_column()` instead. --- Backtrace: ▆ 1. ├─... %>% as.data.frame() 2. ├─base::as.data.frame(.) 3. ├─dplyr::mutate(., Time.X.Treatment = Time * Treat) 4. ├─dplyr::mutate(...) 5. ├─dplyr::mutate(., Subject = paste("S", Subject, sep = "")) 6. ├─dplyr::select(., Sample, Subject, Time, Response, Treat) 7. ├─dplyr::mutate(...) 8. ├─dplyr::left_join(...) 9. ├─dplyr::select(., Subject) 10. ├─dplyr::filter(., count == 4) 11. ├─dplyr::summarise(., count = n()) 12. ├─dplyr::group_by(., Subject) 13. ├─dplyr::select(., Sample, Time, Subject, Response, Treatment.Specific) 14. ├─dplyr::filter(., Treatment.Specific != "PEN") 15. ├─dplyr::left_join(...) 16. ├─dplyr:::left_join.data.frame(...) 17. │ └─dplyr::auto_copy(x, y, copy = copy) 18. │ ├─dplyr::same_src(x, y) 19. │ └─dplyr:::same_src.data.frame(x, y) 20. │ └─base::is.data.frame(y) 21. └─dplyr::add_rownames(sample.info, var = "Sample") 22. └─lifecycle::deprecate_stop("1.0.0", "add_rownames()", "tibble::rownames_to_column()") 23. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'zibr.Rmd' failed with diagnostics: `add_rownames()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::rownames_to_column()` instead. --- failed re-building ‘zibr.Rmd’ SUMMARY: processing the following file failed: ‘zibr.Rmd’ Error: Vignette re-building failed. Execution halted