* using log directory ‘/srv/hornik/tmp/CRAN_pretest/fwtraits.Rcheck’ * using R Under development (unstable) (2025-10-28 r88973) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘fwtraits/DESCRIPTION’ ... OK * this is package ‘fwtraits’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/125s] NOTE Maintainer: ‘Anthony Basooma ’ New submission Possibly misspelled words in DESCRIPTION: Freshwaterecology (13:60) Found the following (possibly) invalid URLs: URL: http://www.gnu.org/licenses/gpl-3.0.html From: README.md Status: Error Message: Timeout was reached [www.gnu.org]: Connection timed out after 60002 milliseconds URL: https://codecov.io/gh/AnthonyBasooma/fwtraits (moved to https://app.codecov.io/gh/AnthonyBasooma/fwtraits) From: README.md Status: 301 Message: Moved Permanently URL: https://github.com/AnthonyBasooma/fwtraits/repo/releases From: README.md Status: 404 Message: Not Found For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘Extract Species Ecological Parameters From www.freshwaterecology.info’ In title case that is: ‘Extract Species Ecological Parameters from Www.freshwaterecology.info’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘fwtraits’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘fw_fdcompute.R’ ‘fw_fdendro.R’ ‘fw_geosites.R’ ‘fw_searchdata.R’ ‘fw_token.R’ ‘fw_vizualize.R’ ‘utils.R’ * 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/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] 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 ... [4s/4s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [2s/2s] ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > > library(testthat) > library(fwtraits) > > test_check("fwtraits") ============================================= ============================================= PLEASE FOLLOW THE INSTRUCTIONS CAREFULLY ============================================= 1. PLEASE EDIT THE .Renviron THATS HAS OPENED == 2. TYPE IN: API_KEY = 36-digits alphanumeric == 3. SAVE AND CLOSE. RESTART RSESSION == 4. CONGS: YOUR ARE READY TO GO!!!!!!!! ============================================ ============================================ [ FAIL 3 | WARN 0 | SKIP 14 | PASS 17 ] ══ Skipped tests (14) ══════════════════════════════════════════════════════════ • On CRAN (14): 'test-fw_visualize.R:5:13', 'test-fwfetchdata.R:8:13', 'test-fwfetchdata.R:21:13', 'test-fwfetchdata.R:30:13', 'test-fwfetchdata.R:57:13', 'test-fwfetchdata.R:81:13', 'test-fwfetchdata.R:97:13', 'test-fwfetchdata.R:119:13', 'test-fwfetchdata.R:138:13', 'test_fwdbguide.R:3:3', 'test_fwfdcompute.R:22:13', 'test_fwregister.R:5:13', 'test_fwtoken.R:3:13', 'test_loaddb.R:4:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-fw_visualize.R:24:1'): (code run outside of `test_that()`) ───── Error: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. Backtrace: ▆ 1. └─fwtraits::fw_fetchdata(...) at test-fw_visualize.R:24:1 2. └─fwtraits::fw_searchdata(...) 3. └─fwtraits::fw_token(...) 4. └─fwtraits::fw_keyload() ── Error ('test_fwsearch.R:9:13'): tchecks ───────────────────────────────────── Error: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_fwsearch.R:9:13 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. └─fwtraits::fw_searchdata(...) 8. └─fwtraits::fw_token(...) 9. └─fwtraits::fw_keyload() ── Error ('test_fwsetapikey.R:22:12'): The key is properly set ───────────────── Error: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. Backtrace: ▆ 1. ├─testthat::expect_equal(nchar(fw_keyload()), 36) at test_fwsetapikey.R:22:12 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nchar(fw_keyload()) 5. └─fwtraits::fw_keyload() [ FAIL 3 | WARN 0 | SKIP 14 | PASS 17 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [6s/6s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘Secure_API_key.Rmd’ using rmarkdown Quitting from Secure_API_key.Rmd:40-53 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- Backtrace: ▆ 1. └─fwtraits::fw_fetchdata(...) 2. └─fwtraits::fw_searchdata(...) 3. └─fwtraits::fw_token(...) 4. └─fwtraits::fw_keyload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Secure_API_key.Rmd' failed with diagnostics: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- failed re-building ‘Secure_API_key.Rmd’ --- re-building ‘data_for_taxa_groups.Rmd’ using rmarkdown Quitting from data_for_taxa_groups.Rmd:86-93 [Retrieve fish species data for one species] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- Backtrace: ▆ 1. └─fwtraits::fw_fetchdata(...) 2. └─fwtraits::fw_searchdata(...) 3. └─fwtraits::fw_token(...) 4. └─fwtraits::fw_keyload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'data_for_taxa_groups.Rmd' failed with diagnostics: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- failed re-building ‘data_for_taxa_groups.Rmd’ --- re-building ‘fishcompute.Rmd’ using rmarkdown Quitting from fishcompute.Rmd:49-56 [retrievedata] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- Backtrace: ▆ 1. └─fwtraits::fw_fetchdata(...) 2. └─fwtraits::fw_searchdata(...) 3. └─fwtraits::fw_token(...) 4. └─fwtraits::fw_keyload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'fishcompute.Rmd' failed with diagnostics: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- failed re-building ‘fishcompute.Rmd’ --- re-building ‘functiondendo.Rmd’ using rmarkdown Quitting from functiondendo.Rmd:43-51 [dataretrieval] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- Backtrace: ▆ 1. └─fwtraits::fw_fetchdata(...) 2. └─fwtraits::fw_searchdata(...) 3. └─fwtraits::fw_token(...) 4. └─fwtraits::fw_keyload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'functiondendo.Rmd' failed with diagnostics: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- failed re-building ‘functiondendo.Rmd’ --- re-building ‘macroinverts.Rmd’ using rmarkdown Quitting from macroinverts.Rmd:55-61 [retrievedata] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- Backtrace: ▆ 1. └─fwtraits::fw_fetchdata(...) 2. └─fwtraits::fw_searchdata(...) 3. └─fwtraits::fw_token(...) 4. └─fwtraits::fw_keyload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'macroinverts.Rmd' failed with diagnostics: The API key has not been well set in the .Renviron file. Run fw_setapikey() and follow the instruction carefully. --- failed re-building ‘macroinverts.Rmd’ SUMMARY: processing the following files failed: ‘Secure_API_key.Rmd’ ‘data_for_taxa_groups.Rmd’ ‘fishcompute.Rmd’ ‘functiondendo.Rmd’ ‘macroinverts.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 2 NOTEs