* using log directory 'd:/Rcompile/CRANpkg/local/4.5/neotoma2.Rcheck' * using R Under development (unstable) (2025-03-11 r87944 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'neotoma2/DESCRIPTION' ... OK * this is package 'neotoma2' version '1.0.5' * 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 'neotoma2' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [10s] OK * checking Rd files ... [3s] 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [13s] ERROR Running examples in 'neotoma2-Ex.R' failed The error most likely occurred in: > ### Name: cite_data,sites-method > ### Title: Obtain data citations from multiple records. > ### Aliases: cite_data,sites-method > > ### ** Examples > > { + ds <- get_datasets(1) + cite_data(ds) + } Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in neotoma2::parseURL(base_url, ...) : object 'response' not found Calls: get_datasets -> get_datasets.numeric -> Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [95s] ERROR Running 'testthat.R' [95s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(neotoma2) Attaching package: 'neotoma2' The following object is masked from 'package:stats': filter > > test_check("neotoma2") Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [api.neotomadb.org]: SSL/TLS connection timeout [ FAIL 8 | WARN 0 | SKIP 48 | PASS 10 ] ══ Skipped tests (48) ══════════════════════════════════════════════════════════ • On CRAN (48): 'test-toJSON.R:2:3', 'test_c.R:10:3', 'test_check_contacts.R:10:3', 'test_chroncontrols.R:5:3', 'test_chroncontrols.R:22:3', 'test_chroncontrols.R:36:3', 'test_clean.R:5:3', 'test_datasets.R:3:3', 'test_datasets.R:19:3', 'test_datasets.R:39:3', 'test_datasets.R:86:3', 'test_datasets.R:109:3', 'test_download.R:3:3', 'test_download.R:32:3', 'test_examples.R:3:3', 'test_filter.R:4:3', 'test_filter.R:27:3', 'test_filter.R:50:3', 'test_filter.R:74:3', 'test_filter.R:111:3', 'test_filter.R:138:3', 'test_filter.R:166:3', 'test_filter.R:192:3', 'test_filter.R:208:3', 'test_filter.R:223:3', 'test_generaltests.R:6:3', 'test_generaltests.R:17:3', 'test_generaltests.R:22:3', 'test_generaltests.R:40:3', 'test_generaltests.R:70:3', 'test_generaltests.R:78:5', 'test_generaltests.R:99:3', 'test_methods.R:3:3', 'test_plotLeaflet.r:6:3', 'test_plotLeaflet.r:18:3', 'test_samples.R:11:3', 'test_setsample.R:8:3', 'test_setsite.r:8:3', 'test_sites.R:9:3', 'test_sites.R:21:3', 'test_sites.R:37:3', 'test_sites.R:49:3', 'test_sites.R:62:3', 'test_sites.R:90:3', 'test_specimens.R:3:3', 'test_specimens.R:11:3', 'test_specimens.R:18:3', 'test_toWide.R:10:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-get_contacts.R:2:3'): Non integer x returns nothing: ─────────── Error in `parseURL(baseURL, ...)`: object 'response' not found Backtrace: ▆ 1. ├─neotoma2::get_contacts(x = "Goring") at test-get_contacts.R:2:3 2. ├─neotoma2:::get_contacts.default(x = "Goring") 3. │ ├─parseURL(baseURL, ...) %>% cleanNULL() 4. │ └─neotoma2::parseURL(baseURL, ...) 5. └─neotoma2:::cleanNULL(.) 6. └─base::rapply(...) ── Error ('test-get_contacts.R:7:3'): Integer x returns sets of contacts: ────── Error in `parseURL(baseURL)`: object 'response' not found Backtrace: ▆ 1. ├─neotoma2::get_contacts(x = 1) at test-get_contacts.R:7:3 2. ├─neotoma2:::get_contacts.numeric(x = 1) 3. │ ├─parseURL(baseURL) %>% cleanNULL() 4. │ └─neotoma2::parseURL(baseURL) 5. └─neotoma2:::cleanNULL(.) 6. └─base::rapply(...) ── Error ('test-get_table.R:6:3'): Call a single database table: ─────────────── Error in `parseURL(paste0("dbtables/table?table=", x, "&limit=", limit, "&offset=", offset))`: object 'response' not found Backtrace: ▆ 1. ├─testthat::expect_is(get_table("agetypes"), "data.frame") at test-get_table.R:6:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─neotoma2::get_table("agetypes") 5. └─neotoma2::parseURL(...) ── Error ('test-get_table.R:11:3'): We can apply the limits for get_table() ──── Error in `parseURL(paste0("dbtables/table?table=", x, "&limit=", limit, "&offset=", offset))`: object 'response' not found Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-get_table.R:11:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(get_table("agetypes", limit = 1)) 5. └─neotoma2::get_table("agetypes", limit = 1) 6. └─neotoma2::parseURL(...) ── Error ('test-get_table.R:16:3'): Limit and offsets work for the get_table() call ── Error in `parseURL(paste0("dbtables/table?table=", x, "&limit=", limit, "&offset=", offset))`: object 'response' not found Backtrace: ▆ 1. ├─testthat::expect_false(...) at test-get_table.R:16:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─rlang::hash(get_table("agetypes", limit = 1)) 5. └─neotoma2::get_table("agetypes", limit = 1) 6. └─neotoma2::parseURL(...) ── Error ('test-ping.R:5:3'): The Pings work ─────────────────────────────────── Error in `ping_head$status_code`: $ operator is invalid for atomic vectors Backtrace: ▆ 1. └─testthat::expect_equal(ping_head$status_code, ping_call$status_code) at test-ping.R:5:3 2. └─testthat::quasi_label(enquo(object), label, arg = "object") 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test_generaltests.R:65:3'): A faunmap dataset with some contacts actually works ── Error in `parseURL(base_url, ...)`: object 'response' not found Backtrace: ▆ 1. ├─neotoma2::get_downloads(7032) at test_generaltests.R:65:3 2. └─neotoma2:::get_downloads.numeric(7032) 3. └─neotoma2::parseURL(base_url, ...) ── Error ('test_generaltests.R:115:3'): Testing the publications calls. ──────── Error in `parseURL(baseURL, ...)`: object 'response' not found Backtrace: ▆ 1. ├─neotoma2::get_publications() at test_generaltests.R:115:3 2. ├─neotoma2:::get_publications.default() 3. │ ├─... %>% pluck("result") 4. │ └─neotoma2::parseURL(baseURL, ...) 5. ├─purrr::pluck(., "result") 6. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default) 7. ├─purrr::pluck(., "data") 8. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default) 9. └─neotoma2:::cleanNULL(.) 10. └─base::rapply(...) [ FAIL 8 | WARN 0 | SKIP 48 | PASS 10 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s] ERROR Error(s) in re-building vignettes: --- re-building 'neotoma2-package.Rmd' using rmarkdown Quitting from lines 77-84 [getSiteBySiteID] (neotoma2-package.Rmd) Error: processing vignette 'neotoma2-package.Rmd' failed with diagnostics: object 'response' not found --- failed re-building 'neotoma2-package.Rmd' SUMMARY: processing the following file failed: 'neotoma2-package.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [26s] OK * checking HTML version of manual ... [33s] OK * DONE Status: 3 ERRORs