Package check result: NOTE Check: compiled code, Result: NOTE File ‘curl/libs/curl.so’: Found non-API call to R: ‘R_new_custom_connection’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. Changes to worse in reverse depends: Package: BFS Check: tests New result: ERROR Running ‘testthat.R’ [18s/127s] 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(BFS) > > test_check("BFS") ==>---------------------------- 7% | ETA: 23s ======>------------------------ 19% | ETA: 20s =========>--------------------- 32% | ETA: 17s =============>----------------- 42% | ETA: 15s ================>-------------- 54% | ETA: 12s ====================>---------- 66% | ETA: 9s =======================>------- 78% | ETA: 6s ===========================>--- 91% | ETA: 2s [ FAIL 7 | WARN 1 | SKIP 0 | PASS 38 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-bfs_get_base_maps.R:5:3'): Get Switzerland base map data as sf works ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "suis") at test-bfs_get_base_maps.R:5:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) ── Error ('test-bfs_get_base_maps.R:13:3'): Get Cantons base map data as sf works ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "kant") at test-bfs_get_base_maps.R:13:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) ── Error ('test-bfs_get_base_maps.R:21:3'): Get Canton Capitals base map data as sf works ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "stkt", type = "Pnts", category = "kk") at test-bfs_get_base_maps.R:21:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) ── Error ('test-bfs_get_base_maps.R:29:3'): Get Lake base map data as sf works ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "seen", category = "11") at test-bfs_get_base_maps.R:29:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) ── Error ('test-bfs_get_base_maps.R:43:3'): bfs_get_base_maps() with gf_ch category ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "suis", category = "gf_ch") at test-bfs_get_base_maps.R:43:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) ── Error ('test-bfs_get_base_maps.R:51:3'): bfs_get_base_maps() with 'polg' geom and date ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: argument is of length zero Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "polg", date = "20230101") at test-bfs_get_base_maps.R:51:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) ── Error ('test-bfs_get_base_maps.R:59:3'): bfs_get_base_maps() with 'polg' geom and recent date different ── Error in `if (nchar(dsn) < 1) stop("`dsn` must point to a source, not an empty string.", call. = FALSE)`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. └─BFS::bfs_get_base_maps(geom = "kant", most_recent = TRUE) at test-bfs_get_base_maps.R:59:3 2. └─sf::read_sf(file_selected) 3. ├─sf::st_read(...) 4. └─sf:::st_read.character(...) [ FAIL 7 | WARN 1 | SKIP 0 | PASS 38 ] Error: Test failures Execution halted Package: chemodiv Check: examples New result: ERROR Running examples in ‘chemodiv-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: NPCTable > ### Title: Generate NPClassifier classification > ### Aliases: NPCTable > > ### ** Examples > > data(minimalCompData) > NPCTable(minimalCompData) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [npclassifier.ucsd.edu]: SSL connection timeout Calls: NPCTable ... request_fetch.write_memory -> -> raise_libcurl_error Execution halted Package: CongressData Check: examples New result: ERROR Running examples in ‘CongressData-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_var_info > ### Title: Get information regarding CongressData variables > ### Aliases: get_var_info > > ### ** Examples > > > # returns all variable information > get_var_info() Error in curl::curl_download(cb_url, cb_temp, mode = "wb") : Timeout was reached [ippsr.msu.edu]: SSL connection timeout Calls: get_var_info -> -> raise_libcurl_error Execution halted Package: kmeRtone Check: tests New result: ERROR Running ‘testthat.R’ [10s/152s] 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(kmeRtone) > > testthat::test_check("kmeRtone") ------------------------------------------------------------ Extraction of Case K-mers ------------------------------------------------------------ % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 3 18.6M 3 687k 0 0 459k 0 0:00:41 0:00:01 0:00:40 459k 82 18.6M 82 15.3M 0 0 6649k 0 0:00:02 0:00:02 --:--:-- 6648k 100 18.6M 100 18.6M 0 0 7499k 0 0:00:02 0:00:02 --:--:-- 7499k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 11.0M 0 31893 0 0 38137 0 0:05:02 --:--:-- 0:05:02 38103 28 11.0M 28 3203k 0 0 1746k 0 0:00:06 0:00:01 0:00:05 1746k 100 11.0M 100 11.0M 0 0 5146k 0 0:00:02 0:00:02 --:--:-- 5147k Extracting 2-mers from chr20............DONE! -- 43.92 secs Extracting 2-mers from chr21............DONE! -- 42.11 secs Extracting 2-mers from chr22............ Downloading chr20.fa.gz from UCSC... Downloading chr21.fa.gz from UCSC... [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_score.R:25:1'): (code run outside of `test_that()`) ──────────── Error in `download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress)`: cannot open URL 'https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/' Backtrace: ▆ 1. └─kmeRtone::kmeRtone(...) at test_score.R:25:1 2. └─kmeRtone::SCORE(...) 3. └─kmeRtone::extractKmers(...) 4. └─future.apply::future_lapply(...) 5. └─future.apply:::future_xapply(...) 6. ├─future::value(fs) 7. └─future:::value.list(fs) 8. ├─future::resolve(...) 9. └─future:::resolve.list(...) 10. └─future (local) signalConditionsASAP(obj, resignal = FALSE, pos = ii) 11. └─future:::signalConditions(...) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted Package: palaeoverse Check: tests New result: ERROR Running ‘testthat.R’ [74s/124s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(palaeoverse) > > test_check("palaeoverse") Loading required package: ape Loading required package: maps Presence of occurrences falling on boundaries detected. Occurrences assigned to upper bin. Average spacing between adjacent cells in the primary grid was set to 274.09 km. H3 resolution: 2 Average spacing between adjacent cells in the primary grid was set to 725.17 km. H3 resolution: 1 Average spacing between adjacent cells in the primary grid was set to 274.09 km. H3 resolution: 2 Average spacing between adjacent cells in the primary grid was set to 725.17 km. H3 resolution: 1 Bin size set to 12 degrees to fit latitudinal range. Bin size set to 12 degrees to fit latitudinal range. Target equal length time bins was set to 10.02 Myr. Generated time bins have a mean length of 10.82 Myr and a standard deviation of 2.41 Myr. Target equal length time bins was set to 6.01 Myr. Generated time bins have a mean length of 7.31 Myr and a standard deviation of 2.98 Myr. Target equal length time bins was set to 10.02 Myr. Generated time bins have a mean length of 10.61 Myr and a standard deviation of 2.52 Myr. Target equal length time bins was set to 20.13 Myr. Generated time bins have a mean length of 50.33 Myr and a standard deviation of 23.5 Myr. Target equal length time bins was set to 10.02 Myr. Generated time bins have a mean length of 10.82 Myr and a standard deviation of 2.41 Myr. Target equal length time bins was set to 49.18 Myr. Generated time bins have a mean length of 49.18 Myr and a standard deviation of 3.18 Myr. Target equal length time bins was set to 24.59 Myr. Generated time bins have a mean length of 24.59 Myr and a standard deviation of 3.08 Myr. Target equal length time bins was set to 13.25 Myr. Generated time bins have a mean length of 13.25 Myr and a standard deviation of 4.11 Myr. [ FAIL 1 | WARN 1 | SKIP 13 | PASS 314 ] ══ Skipped tests (13) ══════════════════════════════════════════════════════════ • On CRAN (13): 'test-axis_geo.R:2:3', 'test-axis_geo.R:15:3', 'test-axis_geo.R:29:3', 'test-axis_geo.R:72:3', 'test-lat_bins_area.R:20:3', 'test-palaeorotate.R:26:3', 'test-palaeorotate.R:82:3', 'test-tax_range_strat.R:26:3', 'test-tax_range_strat.R:38:3', 'test-tax_range_strat.R:50:3', 'test-tax_range_strat.R:62:3', 'test-tax_range_strat.R:74:3', 'test-time_bins.R:3:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-axis_geo.R:61:5'): axis_geo() can be used on multiple sides ──── Error: `name` does not match a built-in or Macrostrat time scale. Backtrace: ▆ 1. └─vdiffr::expect_doppelganger(...) at test-axis_geo.R:46:3 2. └─vdiffr (local) writer(fig, testcase, title) 3. ├─vdiffr:::print_plot(plot, title) 4. └─vdiffr:::print_plot.function(plot, title) 5. └─palaeoverse (local) p() 6. └─palaeoverse::axis_geo(...) at test-axis_geo.R:61:5 7. └─palaeoverse::time_bins(scale = scale_intervals) 8. └─base::tryCatch(...) 9. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. └─value[[3L]](cond) [ FAIL 1 | WARN 1 | SKIP 13 | PASS 314 ] Deleting unused snapshots: • axis_geo/axis-geo-with-backwards-ultrametric-tree.svg • axis_geo/axis-geo-with-downwards-fossil-tree.svg • axis_geo/axis-geo-with-fossil-tree.svg Error: Test failures Execution halted Package: REDCapExporter Check: tests New result: ERROR Running ‘test-as.data.frame.R’ [1s/1s] Running ‘test-build_r_pkg.R’ [3s/3s] Running ‘test-export.R’ [0s/10s] Running ‘test-format_record.R’ [1s/1s] Running ‘test-keyring.R’ [0s/0s] Running the tests in ‘tests/test-export.R’ failed. Complete output: > library(REDCapExporter) > > # Tests rely on publicly available REDCap and tokens published > # https://github.com/redcap-tools/redcap-test-datasets/tree/master > > # project_name token server_url pid server read_only operational notes > # archer 9A81268476645C4E5F03428B8AC3AA7B https://bbmc.ouhsc.edu/redcap/api/ 153 oklahoma-bbmc TRUE TRUE simple structure; read-only > # archer D70F9ACD1EDD6F151C6EA78683944E98 https://bbmc.ouhsc.edu/redcap/api/ 213 oklahoma-bbmc FALSE TRUE simple structure; read & write > # archer 0434F0E9CF53ED0587847AB6E51DE762 https://bbmc.ouhsc.edu/redcap/api/ 212 oklahoma-bbmc TRUE TRUE longitudinal structure; read-only > # archer D72C6485B52FE9F75D27B696977FBA43 https://bbmc.ouhsc.edu/redcap/api/ 268 oklahoma-bbmc TRUE TRUE Russian characters; read-only > > archer01_csv <- export_core(uri = 'https://bbmc.ouhsc.edu/redcap/api/', token = '9A81268476645C4E5F03428B8AC3AA7B') Getting Project Info Error in curl::curl_fetch_memory(uri, handle = h) : Timeout was reached [bbmc.ouhsc.edu]: Failed to connect to bbmc.ouhsc.edu port 443 after 10002 ms: Timeout was reached Calls: export_core ... export_content -> -> raise_libcurl_error Execution halted Package: snvecR Check: tests New result: ERROR Running ‘testthat.R’ [20s/299s] 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(snvecR) > > test_check("snvecR") [ FAIL 1 | WARN 0 | SKIP 2 | PASS 38 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-get_solution.R:22:3', 'test-snvec.R:34:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-get_solution.R:13:3'): get_solution() can load eccentricity solutions ── Error in `open.connection(con, "rb")`: cannot open the connection Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-get_solution.R:13:3 2. └─rlang::cnd_signal(state$error) [ FAIL 1 | WARN 0 | SKIP 2 | PASS 38 ] Error: Test failures Execution halted Package: vcr Check: tests New result: ERROR Running ‘test-all.R’ [5s/15s] Running the tests in ‘tests/test-all.R’ failed. Complete output: > library("testthat") > library('vcr') > test_check("vcr") Timeout was reached [nghttp2.org]: Operation timed out after 10001 milliseconds with 0 bytes received [ FAIL 6 | WARN 2 | SKIP 50 | PASS 450 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • Did not find: '../../man/vcr_configure.Rd' (1): 'test-configuration.R:53:3' • On CRAN (49): 'test-RequestHandler.R:1:1', 'test-RequestIgnorer.R:41:3', 'test-RequestIgnorer.R:83:3', 'test-ause_cassette.R:6:3', 'test-ause_cassette_match_body_empty_body.R:2:3', 'test-ause_cassette_match_query.R:11:3', 'test-ause_cassette_match_requests_on.R:2:3', 'test-ause_cassette_match_requests_on.R:129:3', 'test-ause_cassette_match_requests_on_json.R:6:3', 'test-ause_cassette_match_requests_on_json.R:63:3', 'test-ause_cassette_re_record.R:15:3', 'test-ause_cassette_record_modes.R:13:3', 'test-ause_cassette_record_modes.R:54:3', 'test-ause_cassette_record_modes.R:80:3', 'test-ause_cassette_record_modes.R:126:3', 'test-ause_cassette_write_to_disk.R:8:3', 'test-ause_cassette_write_to_disk.R:39:3', 'test-ause_cassette_write_to_disk.R:67:3', 'test-ause_cassette_write_to_disk_binary_files.R:7:3', 'test-ause_cassette_write_to_disk_binary_files.R:42:3', 'test-ause_cassette_write_to_disk_binary_files.R:104:3', 'test-binary_images.R:7:3', 'test-binary_images.R:57:3', 'test-check_cassette_names.R:2:3', 'test-crul.R:1:1', 'test-filter-sensitive-strings.R:1:1', 'test-filter_headers.R:4:3', 'test-filter_headers.R:61:3', 'test-filter_headers.R:106:3', 'test-filter_headers.R:138:3', 'test-filter_headers.R:185:3', 'test-filter_headers.R:233:3', 'test-filter_query_parameters.R:10:3', 'test-filter_query_parameters.R:57:3', 'test-filter_query_parameters.R:104:3', 'test-filter_query_parameters.R:154:3', 'test-filter_query_parameters.R:199:3', 'test-httr.R:1:1', 'test-httr2.R:1:1', 'test-request_summary.R:10:3', 'test-response_summary.R:13:3', 'test-response_summary.R:29:3', 'test-response_summary.R:47:3', 'test-serializers_json.R:22:3', 'test-use_vcr.R:4:3', 'test-vcr_test_path.R:2:3', 'test-vcr_test_path.R:24:3', 'test-vcr_test_path.R:46:3', 'test-write_disk_path_package_context.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-HttpInteraction.R:9:3'): HttpInteraction ─────────────────────── Error in `curl::curl_fetch_memory(x$url$url, handle = x$url$handle)`: URL using bad/illegal format or missing URL: URL rejected: No host part in the URL Backtrace: ▆ 1. ├─cli$post(body = body) at test-HttpInteraction.R:9:3 2. │ └─private$make_request(rr) 3. │ └─crul:::crul_fetch(opts) 4. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle) 5. └─curl:::raise_libcurl_error(...) ── Error ('test-HttpInteractionList.R:9:3'): HTTPInteractionList ─────────────── Error in `curl::curl_fetch_memory(x$url$url, handle = x$url$handle)`: URL using bad/illegal format or missing URL: URL rejected: No host part in the URL Backtrace: ▆ 1. ├─cli$post(body = body) at test-HttpInteractionList.R:9:3 2. │ └─private$make_request(rr) 3. │ └─crul:::crul_fetch(opts) 4. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle) 5. └─curl:::raise_libcurl_error(...) ── Error ('test-issues.R:3:5'): issue 249 is correctly handled. ──────────────── Error in `curl::curl_fetch_memory(url, handle = handle)`: URL using bad/illegal format or missing URL: URL rejected: Port number was not a decimal number between 0 and 65535 Backtrace: ▆ 1. ├─vcr::use_cassette(...) at test-issues.R:2:3 2. │ └─cassette$call_block(...) 3. ├─httr::GET(hb("/status/401")) at test-issues.R:3:5 4. │ └─httr:::request_perform(req, hu$handle$handle) 5. │ └─httr:::perform_callback("request", req = req) 6. │ └─webmockr (local) callback(...) 7. │ └─webmockr::HttrAdapter$new()$handle_request(req) 8. │ └─private$request_handler(req)$handle() 9. │ └─eval(parse(text = req_type_fun))(self$request) 10. │ └─eval(parse(text = paste0("httr::", self$request_original$method)))(...) 11. │ └─httr:::request_perform(req, hu$handle$handle) 12. │ ├─httr:::request_fetch(req$output, req$url, handle) 13. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle) 14. │ └─curl::curl_fetch_memory(url, handle = handle) 15. └─curl:::raise_libcurl_error(...) ── Error ('test-lightswitch.R:140:5'): turned_off ────────────────────────────── Error in `curl::curl_fetch_memory(x$url$url, handle = x$url$handle)`: URL using bad/illegal format or missing URL: URL rejected: No host part in the URL Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-lightswitch.R:139:3 2. │ └─base::withCallingHandlers(...) 3. ├─vcr::turned_off(...) 4. │ └─base::force(...) 5. ├─crul::HttpClient$new(url = hb("/get"))$get() at test-lightswitch.R:140:5 6. │ └─private$make_request(rr) 7. │ └─crul:::crul_fetch(opts) 8. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle) 9. └─curl:::raise_libcurl_error(...) ── Error ('test-quiet.R:11:3'): quiet works ──────────────────────────────────── Error in `curl::curl_fetch_memory(x$url$url, handle = x$url$handle)`: URL using bad/illegal format or missing URL: URL rejected: No host part in the URL Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-quiet.R:11:3 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. ├─vcr::use_cassette("foo3", con$get("get")) 7. │ └─cassette$call_block(...) 8. ├─con$get("get") 9. │ └─private$make_request(rr) 10. │ └─adap$handle_request(opts) 11. │ └─private$request_handler(req)$handle() 12. │ └─eval(parse(text = req_type_fun))(self$request) 13. │ └─webmockr::webmockr_crul_fetch(self$request_original) 14. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle) 15. └─curl:::raise_libcurl_error(...) ── Error ('test-serializers.R:22:5'): you can record a new cassette of same name with different serializer ── Error in `curl::curl_fetch_memory(x$url$url, handle = x$url$handle)`: URL using bad/illegal format or missing URL: URL rejected: No host part in the URL Backtrace: ▆ 1. ├─vcr::use_cassette(...) at test-serializers.R:21:3 2. │ └─cassette$call_block(...) 3. ├─crul::HttpClient$new(hb("/get"))$get() at test-serializers.R:22:5 4. │ └─private$make_request(rr) 5. │ └─adap$handle_request(opts) 6. │ └─private$request_handler(req)$handle() 7. │ └─eval(parse(text = req_type_fun))(self$request) 8. │ └─webmockr::webmockr_crul_fetch(self$request_original) 9. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle) 10. └─curl:::raise_libcurl_error(...) [ FAIL 6 | WARN 2 | SKIP 50 | PASS 450 ] Error: Test failures Execution halted Ran 68/68 deferred expressions