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### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TaxSEA.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings TaxSEA_1.1.8.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/TaxSEA.Rcheck'
* using R version 4.5.1 (2025-06-13 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
* using option '--no-vignettes'
* checking for file 'TaxSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TaxSEA' version '1.1.8'
* 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 'TaxSEA' 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 ... 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 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 ... NOTE
TaxSEA: no visible binding for global variable 'TaxSEA_db'
TaxSEA: no visible global function definition for 'stack'
get_ncbi_taxon_ids : get_ncbi_taxon_id: no visible global function
  definition for 'URLencode'
get_ncbi_taxon_ids: no visible binding for global variable 'NCBI_ids'
get_taxon_sets: no visible binding for global variable 'TaxSEA_db'
get_taxon_sets: no visible binding for global variable 'NCBI_ids'
Undefined global functions or variables:
  NCBI_ids TaxSEA_db URLencode stack
Consider adding
  importFrom("utils", "URLencode", "stack")
to your NAMESPACE file.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
TaxSEA 4.36   0.38    5.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TaxSEA)
  > test_check("TaxSEA")
  Using cached version from 2025-04-24 21:51:05
  [ FAIL 1 | WARN 10 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-TaxSEA.R:6:3'): TaxSEA returns valid output with test data ───
  Names of `res` ('All_databases', 'Metabolite_producers', 'Health_associations', 'BacDive_bacterial_physiology', 'BugSigDB', 'Gut_Brain_Modules_VallesColomer2019') don't match 'All_databases', 'Metabolite_producers', 'Health_associations', 'BacDive_bacterial_physiology', 'Gut_Brain_Modules_VallesColomer2019', 'BugSigDB'
  
  [ FAIL 1 | WARN 10 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/TaxSEA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL TaxSEA
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'TaxSEA' ...
** this is package 'TaxSEA' version '1.1.8'
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TaxSEA)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TaxSEA)
> test_check("TaxSEA")
Using cached version from 2025-04-24 21:51:05
[ FAIL 1 | WARN 10 | SKIP 0 | PASS 13 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-TaxSEA.R:6:3'): TaxSEA returns valid output with test data ───
Names of `res` ('All_databases', 'Metabolite_producers', 'Health_associations', 'BacDive_bacterial_physiology', 'BugSigDB', 'Gut_Brain_Modules_VallesColomer2019') don't match 'All_databases', 'Metabolite_producers', 'Health_associations', 'BacDive_bacterial_physiology', 'Gut_Brain_Modules_VallesColomer2019', 'BugSigDB'

[ FAIL 1 | WARN 10 | SKIP 0 | PASS 13 ]
Error: Test failures
Execution halted