Package: annotaR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘annotaR-workflow.Rmd’ using rmarkdown Quitting from annotaR-workflow.Rmd:45-56 [annotation] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `.processResults()`: ! Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98. --- Backtrace: ▆ 1. ├─... %>% add_drug_links() 2. ├─annotaR::add_drug_links(.) 3. │ └─"gene" %in% names(annotaR_object) 4. └─annotaR::add_disease_links(.) 5. └─biomaRt::getBM(...) 6. └─biomaRt:::.processResults(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics: Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98. --- failed re-building ‘annotaR-workflow.Rmd’ SUMMARY: processing the following file failed: ‘annotaR-workflow.Rmd’ Error: Vignette re-building failed. Execution halted Package: CohortGenerator Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘CreatingCohortSubsetDefinitions.Rmd’ using rmarkdown --- finished re-building ‘CreatingCohortSubsetDefinitions.Rmd’ --- re-building ‘GeneratingCohorts.Rmd’ using rmarkdown trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Quitting from GeneratingCohorts.Rmd:122-144 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `utils::download.file()`: ! cannot open URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' --- Backtrace: x 1. \-Eunomia::getEunomiaConnectionDetails() 2. \-Eunomia::getDatabaseFile(...) 3. \-Eunomia::downloadEunomiaData(...) 4. \-utils::download.file(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'GeneratingCohorts.Rmd' failed with diagnostics: cannot open URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' --- failed re-building ‘GeneratingCohorts.Rmd’ --- re-building ‘SamplingCohorts.Rmd’ using rmarkdown --- finished re-building ‘SamplingCohorts.Rmd’ --- re-building ‘UsingTemplateCohorts.Rmd’ using rmarkdown trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Quitting from UsingTemplateCohorts.Rmd:40-72 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `utils::download.file()`: ! cannot open URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' --- Backtrace: ▆ 1. ├─DatabaseConnector::connect(Eunomia::getEunomiaConnectionDetails()) 2. └─Eunomia::getEunomiaConnectionDetails() 3. └─Eunomia::getDatabaseFile(...) 4. └─Eunomia::downloadEunomiaData(...) 5. └─utils::download.file(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'UsingTemplateCohorts.Rmd' failed with diagnostics: cannot open URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' --- failed re-building ‘UsingTemplateCohorts.Rmd’ SUMMARY: processing the following files failed: ‘GeneratingCohorts.Rmd’ ‘UsingTemplateCohorts.Rmd’ Error: Vignette re-building failed. Execution halted Package: CohortGenerator Check: tests New result: ERROR Running ‘testthat.R’ [3s/7s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CohortGenerator) Loading required package: DatabaseConnector Loading required package: R6 > > test_check("CohortGenerator") attempting to download GiBleed trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Error in `source_dir()`: ! Failed to evaluate './setup.R'. Caused by error in `utils::download.file()`: ! cannot open URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Backtrace: ▆ 1. ├─testthat::test_check("CohortGenerator") 2. │ └─testthat::test_dir(...) 3. │ └─testthat:::test_files(...) 4. │ └─testthat:::test_files_serial(...) 5. │ └─testthat:::test_files_setup_state(...) 6. │ └─testthat::source_test_setup(".", env) 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) 8. │ └─base::lapply(...) 9. │ └─testthat (local) FUN(X[[i]], ...) 10. │ └─testthat::source_file(...) 11. │ ├─base::withCallingHandlers(...) 12. │ └─base::eval(exprs, env) 13. │ └─base::eval(exprs, env) 14. │ └─Eunomia::getEunomiaConnectionDetails() at ./setup.R:2:1 15. │ └─Eunomia::getDatabaseFile(...) 16. │ └─Eunomia::downloadEunomiaData(...) 17. │ └─utils::download.file(...) 18. └─base::.handleSimpleError(...) 19. └─testthat (local) h(simpleError(msg, call)) 20. └─cli::cli_abort(...) 21. └─rlang::abort(...) Warning message: In utils::download.file(url = paste(baseUrl, datasetName, zipName, : cannot open URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip': HTTP status was '429 Unknown Error' Execution halted Package: ebvcube Check: tests New result: ERROR Running ‘testthat.R’ [40s/59s] 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(ebvcube) ebvcube 0.5.2 > > test_check("ebvcube") Warning: stack imbalance in '<-', 77 then 79 Warning: stack imbalance in '{', 73 then 75 Saving _problems/test-download-12.R [ FAIL 1 | WARN 10 | SKIP 0 | PASS 239 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-download.R:12:5'): test ebv_download ID=numeric ──────────────── Error in `curl::curl_download(nc_url, destfile = file.path(outputdir, name_nc), quiet = !verbose)`: Timeout was reached [portal.geobon.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─ebvcube::ebv_download(27, dir, verbose = FALSE) at test-download.R:12:5 2. │ └─curl::curl_download(...) 3. └─curl:::raise_libcurl_error(...) [ FAIL 1 | WARN 10 | SKIP 0 | PASS 239 ] Error: ! Test failures. Execution halted Package: ggpp Check: tests New result: ERROR Running ‘testthat.R’ [156s/157s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ggpp) Loading required package: ggplot2 Registered S3 methods overwritten by 'ggpp': method from heightDetails.titleGrob ggplot2 widthDetails.titleGrob ggplot2 Attaching package: 'ggpp' The following object is masked from 'package:ggplot2': annotate > > # keep error messages as ASCII > options(cli.condition_unicode_bullets = FALSE) > > test_check("ggpp") Saving _problems/test-try_tibble-42.R Saving _problems/test-try_tibble-55.R [ FAIL 2 | WARN 0 | SKIP 71 | PASS 1242 ] ══ Skipped tests (71) ══════════════════════════════════════════════════════════ • Not yet implemented (18): 'test-position_dodge2_keep.R:48:3', 'test-position_dodge2_keep.R:71:3', 'test-position_dodge2nudge.R:56:3', 'test-position_dodge2nudge.R:79:3', 'test-position_dodge2nudge.R:102:3', 'test-position_dodge2nudge.R:124:3', 'test-position_dodge2nudge.R:147:3', 'test-position_dodge2nudge.R:170:3', 'test-position_dodge2nudge_to.R:93:3', 'test-position_dodge2nudge_to.R:120:3', 'test-position_dodge2nudge_to.R:147:3', 'test-position_dodge_keep.R:65:3', 'test-position_dodgenudge.R:40:3', 'test-position_dodgenudge.R:61:3', 'test-position_dodgenudge.R:82:3', 'test-position_dodgenudge.R:103:3', 'test-position_dodgenudge.R:124:3', 'test-position_dodgenudge.R:145:3' • On CRAN (52): 'test-annotate.R:23:1', 'test-annotate.R:47:1', 'test-annotate.R:80:1', 'test-geom-label-pairwise.R:3:1', 'test-geom-label-pairwise.R:65:1', 'test-geom-label-pairwise.R:173:1', 'test-geom-label.R:3:1', 'test-geom-plot.R:57:1', 'test-geom-plot.R:82:1', 'test-geom-quadrant-lines.R:58:1', 'test-geom-table.R:90:1', 'test-geom-table.R:103:1', 'test-geom-table.R:150:1', 'test-geom-table.R:254:1', 'test-geom-table.R:379:1', 'test-geom-table.R:528:1', 'test-geom-table.R:629:1', 'test-geom-table.R:722:1', 'test-geom-table.R:732:1', 'test-geom-text-pairwise.R:3:1', 'test-geom-text-pairwise.R:74:1', 'test-geom-text-pairwise.R:149:1', 'test-geom-text.R:3:1', 'test-geom-text_linked.R:6:1', 'test-geom-text_linked.R:189:1', 'test-geom-text_linked.R:204:1', 'test-geom-text_linked.R:233:1', 'test-position-nudge.R:3:1', 'test-position-nudge.R:66:1', 'test-position-nudge.R:122:1', 'test-position-nudge.R:187:1', 'test-position-nudge.R:239:1', 'test-position-nudge.R:264:1', 'test-position-nudge.R:371:1', 'test-position-nudge.R:396:1', 'test-position-nudge.R:498:1', 'test-position_dodge2nudge.R:174:1', 'test-position_dodge2nudge_to.R:151:1', 'test-position_dodgenudge.R:149:1', 'test-stat-d1d-flt.R:184:1', 'test-stat-d1d-flt.R:308:1', 'test-stat-d1d-flt.R:443:1', 'test-stat-d1d-flt.R:672:1', 'test-stat-d1d-flt.R:806:1', 'test-stat-d1d-flt.R:935:1', 'test-stat-d2d-flt.R:292:1', 'test-stat-d2d-flt.R:431:1', 'test-stat-d2d-flt.R:661:1', 'test-stat_fmt_tb.R:3:1', 'test-stat_panel_counts.R:3:1', 'test-stat_panel_counts.R:59:1', 'test-stat_quadrant_counts.R:5:1' • On Linux (1): 'test-position-nudge.R:438:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-try_tibble.R:41:3'): try_tibble, with xts object with daily data ── Error in `xts(x, order.by = order_by_, frequency = frequency, ...)`: 'order.by' cannot contain 'NA', 'NaN', or 'Inf' Backtrace: ▆ 1. ├─xts::as.xts(data.frame(a = 1:50, t = lubridate::now() + lubridate::days(1:50))) at test-try_tibble.R:41:3 2. └─xts:::as.xts.data.frame(...) 3. └─xts::xts(x, order.by = order_by_, frequency = frequency, ...) ── Error ('test-try_tibble.R:52:3'): try_tibble, with xts object with daily data as Dates ── Error in `xts(x, order.by = order_by_, frequency = frequency, ...)`: 'order.by' cannot contain 'NA', 'NaN', or 'Inf' Backtrace: ▆ 1. ├─xts::as.xts(...) at test-try_tibble.R:52:3 2. └─xts:::as.xts.data.frame(...) 3. └─xts::xts(x, order.by = order_by_, frequency = frequency, ...) [ FAIL 2 | WARN 0 | SKIP 71 | PASS 1242 ] Deleting unused snapshots: 'position-nudge/nudge-line1.svg', 'position-nudge/nudge-line2.svg', 'position-nudge/nudge-line3.svg', 'position-nudge/nudge-line3a.svg', 'position-nudge/nudge-line4.svg', 'position-nudge/nudge-line5.svg', 'position-nudge/nudge-line6.svg', and 'position-nudge/nudge-line7.svg' Error: ! Test failures. Execution halted Package: ROCsurf Check: tests New result: ERROR Running ‘testthat.R’ [129s/130s] 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(ROCsurf) > > test_check("ROCsurf") Saving _problems/testfunction-3759.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 516 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('testfunction.R:3754:3'): function return a double or list ─────────── Error in `r.tc_index(x, y, z, init_param = c(alpha1 = alpha1, beta1 = beta1, alpha2 = alpha2, beta2 = beta2, alpha3 = alpha3, beta3 = beta3), init_index = c(median(x), median(y)), model = c("LLL"), method = c("MLE"))`: Optimization did not converge.Please check your initial parameters. Backtrace: ▆ 1. ├─testthat::expect_type(...) at testfunction.R:3754:3 2. │ └─testthat::quasi_label(enquo(object)) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─ROCsurf::r.tc_index(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 516 ] Error: ! Test failures. Execution halted Package: tidytlg Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘freq.Rmd’ using rmarkdown --- finished re-building ‘freq.Rmd’ --- re-building ‘symbols.Rmd’ using rmarkdown --- finished re-building ‘symbols.Rmd’ --- re-building ‘tbl_manipulation.Rmd’ using rmarkdown --- finished re-building ‘tbl_manipulation.Rmd’ --- re-building ‘tidytlg.Rmd’ using rmarkdown Quitting from tidytlg.Rmd:83-92 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `open.connection()`: ! cannot open the connection to 'https://github.com/phuse-org/TestDataFactory/raw/refs/heads/main/Updated/TDF_ADaM/adsl.xpt' --- Backtrace: ▆ 1. └─haven::read_xpt(url(testdata)) 2. └─readr::datasource(file) 3. └─readr:::datasource_connection(...) 4. └─readr:::read_connection(path) 5. ├─base::open(con, "rb") 6. └─base::open.connection(con, "rb") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tidytlg.Rmd' failed with diagnostics: cannot open the connection to 'https://github.com/phuse-org/TestDataFactory/raw/refs/heads/main/Updated/TDF_ADaM/adsl.xpt' --- failed re-building ‘tidytlg.Rmd’ --- re-building ‘tlgsetup.Rmd’ using rmarkdown --- finished re-building ‘tlgsetup.Rmd’ --- re-building ‘univar.Rmd’ using rmarkdown --- finished re-building ‘univar.Rmd’ SUMMARY: processing the following file failed: ‘tidytlg.Rmd’ Error: Vignette re-building failed. Execution halted