* using log directory ‘/Users/ripley/R/packages/tests-devel/rtreeoflife.Rcheck’
* using R Under development (unstable) (2026-08-04 r90348)
* using platform: aarch64-apple-darwin25.6.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.1.1.101)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.6
* using session charset: UTF-8
* current time: 2026-08-04 12:47:33 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘rtreeoflife/DESCRIPTION’ ... OK
* this is package ‘rtreeoflife’ version ‘0.1.0’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtreeoflife’ can be installed ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
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(rtreeoflife)
  ── Attaching rtreeoflife ────────────────────────────────── rtreeoflife 0.1.0 ──
  ✔ species index       tol_species_index(), tol_match_species()
  ✔ selective download  tol_download_fasta(), tol_export_fasta()
  ✔ tidy FASTA          tol_attach_fasta(), tol_fasta_long()
  ✔ visualisation       tol_plot_gene_recovery(), tol_plot_tree()
  ℹ Data source: <https://treeoflife.kew.org/> and <https://sftp.kew.org/pub/treeoflife/current_release/>
  > 
  > test_check("rtreeoflife")
  Saving _problems/test-species-135.R
  Saving _problems/test-species-152.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-species.R:135:3'): FASTA resolution uses a temporary directory by default ──
  Expected `startsWith(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-species.R:152:3'): download FASTA validate_only does not write a manifest by default for temp files ──
  Expected `startsWith(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/rtreeoflife.Rcheck/00check.log’
for details.

       18.70 real        14.14 user         3.82 sys