• using R version 4.6.1 (2026-06-24 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 14.3.0     GNU Fortran (GCC) 14.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8 * current time: 2026-09-30 03:44:41 UTC
• checking for file 'shinyscholar/DESCRIPTION' ... OK
• this is package 'shinyscholar' version '0.4.5'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'shinyscholar' can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s] OK
• checking whether the package can be unloaded cleanly ... [0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s] OK
• checking loading without being on the library search path ... [0s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE renv was unable to query available packages from the following repositories: - # https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib ------------- error downloading 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/PACKAGES.rds' [error code 22] error downloading 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/PACKAGES.gz' [error code 22] error downloading 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/PACKAGES' [error code 22]
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [4s] OK
• checking Rd files ... [1s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... [0s] ERROR Running examples in 'shinyscholar-Ex.R' failed The error most likely occurred in: > ### Name: create_template > ### Title: Create a skeleton application containing empty modules > ### Aliases: create_template > > ### ** Examples > > td <- tempfile() > dir.create(td, recursive = TRUE) > > modules <- data.frame( + "component" = c("data", "data", "plot", "plot"), + "long_component" = c("Load data", "Load data", "Plot data", "Plot data"), + "module" = c("user", "database", "histogram", "scatter"), + "long_module" = c("Upload your own data", "Query a database to obtain data", + "Plot the data as a histogram", "Plot the data as a scatterplot"), + "map" = c(TRUE, TRUE, FALSE, FALSE), + "result" = c(FALSE, FALSE, TRUE, TRUE), + "rmd" = c(TRUE, TRUE, TRUE, TRUE), + "save" = c(TRUE, TRUE, TRUE, TRUE), + "download" = c(FALSE, FALSE, TRUE, TRUE), + "async" = c(TRUE, FALSE, FALSE, FALSE)) > > common_objects = c("raster", "histogram", "scatter") > > create_template(path = td, name = "demo", + common_objects = common_objects, modules = modules, + author = "Simon E. H. Smart", include_map = TRUE, include_table = TRUE, + include_code = TRUE, install = FALSE) Warning in url(sprintf("%s/%s", cran, path), open = "rb") :   cannot open URL 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds': HTTP status was '404 Not Found' Error in url(sprintf("%s/%s", cran, path), open = "rb") :   cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds' Calls: create_template ... <Anonymous> -> as.data.frame -> read_CRAN_object -> gzcon -> url Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [13s] ERROR   Running 'testthat.R' [13s] Running the tests in 'tests/testthat.R' failed. Complete output:   > Sys.setenv("R_TEST" = "")   > library(testthat)   > library(shinyscholar)   > library(shinytest2)   >   > test_check("shinyscholar")   renv was unable to query available packages from the following repositories:   - # https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib -------------   error downloading 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/PACKAGES.rds' [error code 22]   error downloading 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/PACKAGES.gz' [error code 22]   error downloading 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/PACKAGES' [error code 22]         Saving _problems/test-create_template-50.R   Saving _problems/test-create_template-55.R   Saving _problems/test-create_template-60.R   Saving _problems/test-create_template-65.R   Saving _problems/test-create_template-147.R   Saving _problems/test-create_template-192.R   Saving _problems/test-create_template-240.R   Saving _problems/test-create_template-275.R   [ FAIL 8 | WARN 7 | SKIP 26 | PASS 117 ]      ══ Skipped tests (26) ══════════════════════════════════════════════════════════   • On CRAN (26): 'test-downloads.R:6:5', 'test-downloads.R:37:5',     'test-downloads.R:52:5', 'test-downloads.R:71:5', 'test-helpers.R:7:5',     'test-metadata.R:98:5', 'test-plot_auto.R:7:5', 'test-plot_hist.R:20:5',     'test-plot_scatter.R:19:5', 'test-plot_semi.R:6:5',     'test-save_and_load.R:121:5', 'test-save_load.R:6:5',     'test-save_load.R:19:5', 'test-save_load.R:31:5', 'test-save_load.R:47:5',     'test-select_async.R:4:5', 'test-select_async.R:33:5',     'test-select_async.R:44:5', 'test-select_async.R:56:5',     'test-select_query.R:4:5', 'test-select_query.R:35:5',     'test-select_query.R:47:5', 'test-select_query.R:59:5',     'test-select_user.R:15:5', 'test-select_user.R:26:5',     'test-select_user.R:37:5'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-create_template.R:47:3'): Check create template returns expected errors ──   `create_template(...)` threw an error with unexpected message.   Expected match: "A package on CRAN already uses that name"   Actual message: "cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'"   Backtrace:        ▆     1. ├─testthat::expect_error(...) at test-create_template.R:47:3     2. │ └─testthat:::quasi_capture(...)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─shinyscholar::create_template(...)     7. ├─name %in% tools::CRAN_package_db()[, c("Package")]     8. └─tools::CRAN_package_db()     9. ├─base::as.data.frame(...)    10. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    11. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    12. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Failure ('test-create_template.R:52:3'): Check create template returns expected errors ──   `create_template(...)` threw an error with unexpected message.   Expected match: "The specified app directory already exists"   Actual message: "cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'"   Backtrace:        ▆     1. ├─testthat::expect_error(...) at test-create_template.R:52:3     2. │ └─testthat:::quasi_capture(...)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─shinyscholar::create_template(...)     7. ├─name %in% tools::CRAN_package_db()[, c("Package")]     8. └─tools::CRAN_package_db()     9. ├─base::as.data.frame(...)    10. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    11. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    12. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Failure ('test-create_template.R:57:3'): Check create template returns expected errors ──   `create_template(...)` threw an error with unexpected message.   Expected match: "modules must be a dataframe"   Actual message: "cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'"   Backtrace:        ▆     1. ├─testthat::expect_error(...) at test-create_template.R:57:3     2. │ └─testthat:::quasi_capture(...)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─shinyscholar::create_template(...)     7. ├─name %in% tools::CRAN_package_db()[, c("Package")]     8. └─tools::CRAN_package_db()     9. ├─base::as.data.frame(...)    10. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    11. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    12. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Error ('test-create_template.R:62:3'): Check create template returns expected errors ──   Error in `url(sprintf("%s/%s", cran, path), open = "rb")`: cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'   Backtrace:        ▆     1. ├─testthat::expect_warning(...) at test-create_template.R:62:3     2. │ └─testthat:::quasi_capture(...)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─shinyscholar::create_template(...)     7. ├─name %in% tools::CRAN_package_db()[, c("Package")]     8. └─tools::CRAN_package_db()     9. ├─base::as.data.frame(...)    10. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    11. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    12. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Error ('test-create_template.R:145:5'): Check create template function works as expected ──   Error in `url(sprintf("%s/%s", cran, path), open = "rb")`: cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'   Backtrace:       ▆    1. ├─withr::with_temp_libpaths(...) at test-create_template.R:137:3    2. │ └─base::force(code)    3. └─shinyscholar::create_template(...) at test-create_template.R:145:5    4. ├─name %in% tools::CRAN_package_db()[, c("Package")]    5. └─tools::CRAN_package_db()    6. ├─base::as.data.frame(...)    7. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    8. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    9. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Error ('test-create_template.R:189:5'): Check create template function works with false settings ──   Error in `url(sprintf("%s/%s", cran, path), open = "rb")`: cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'   Backtrace:       ▆    1. ├─withr::with_temp_libpaths(...) at test-create_template.R:177:3    2. │ └─base::force(code)    3. └─shinyscholar::create_template(...) at test-create_template.R:189:5    4. ├─name %in% tools::CRAN_package_db()[, c("Package")]    5. └─tools::CRAN_package_db()    6. ├─base::as.data.frame(...)    7. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    8. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    9. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Error ('test-create_template.R:237:7'): Check async, no map runs correctly ──   Error in `url(sprintf("%s/%s", cran, path), open = "rb")`: cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'   Backtrace:       ▆    1. ├─withr::with_temp_libpaths(...) at test-create_template.R:225:5    2. │ └─base::force(code)    3. └─shinyscholar::create_template(...) at test-create_template.R:237:7    4. ├─name %in% tools::CRAN_package_db()[, c("Package")]    5. └─tools::CRAN_package_db()    6. ├─base::as.data.frame(...)    7. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    8. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    9. └─base::url(sprintf("%s/%s", cran, path), open = "rb")   ── Error ('test-create_template.R:272:7'): Check async, with map runs correctly ──   Error in `url(sprintf("%s/%s", cran, path), open = "rb")`: cannot open the connection to 'https://bioconductor.statistik.tu-dortmund.de/cran/web/packages/packages.rds'   Backtrace:       ▆    1. ├─withr::with_temp_libpaths(...) at test-create_template.R:260:5    2. │ └─base::force(code)    3. └─shinyscholar::create_template(...) at test-create_template.R:272:7    4. ├─name %in% tools::CRAN_package_db()[, c("Package")]    5. └─tools::CRAN_package_db()    6. ├─base::as.data.frame(...)    7. └─tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packages/packages.rds")    8. ├─base::gzcon(url(sprintf("%s/%s", cran, path), open = "rb"))    9. └─base::url(sprintf("%s/%s", cran, path), open = "rb")      [ FAIL 8 | WARN 7 | SKIP 26 | PASS 117 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [19s] OK
• checking HTML version of manual ... [4s] OK
• DONE

Status: 2 ERRORs, 1 NOTE