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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:TaxSEA.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings TaxSEA_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/TaxSEA.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-06 09:05:20 UTC
* checking for file ‘TaxSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TaxSEA’ version ‘1.5.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘methods’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_ncbi_taxon_ids : get_ncbi_taxon_id: no visible global function
  definition for ‘URLencode’
get_ncbi_taxon_ids: no visible global function definition for ‘data’
get_ncbi_taxon_ids: no visible binding for global variable ‘NCBI_ids’
get_taxon_sets: no visible global function definition for ‘data’
get_taxon_sets: no visible binding for global variable ‘TaxSEA_db’
get_taxon_sets: no visible binding for global variable ‘NCBI_ids’
ss_prepare: no visible binding for global variable ‘TaxSEA_db’
taxon_rank_sets: no visible global function definition for ‘is’
taxsea_KS : <anonymous>: no visible global function definition for
  ‘median’
taxsea_prepare: no visible binding for global variable ‘TaxSEA_db’
Undefined global functions or variables:
  NCBI_ids TaxSEA_db URLencode data is median
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "median")
  importFrom("utils", "URLencode", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  NCBI_ids.rda     136Kb     42Kb       xz
  TaxSEA_db.rda     48Kb     35Kb    bzip2
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TaxSEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TaxSEA
> ### Title: TaxSEA: Taxon Set Enrichment Analysis
> ### Aliases: TaxSEA
> 
> ### ** Examples
> 
> data("TaxSEA_test_data")
> res <- TaxSEA(taxon_ranks = TaxSEA_test_data)
Error while performing HEAD request.
   Proceeding without cache information.
Error: download failed; see warnings()
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. └─TaxSEA::TaxSEA(TaxSEA_test_data) at test-TaxSEA.R:3:3
   2.   └─TaxSEA:::taxsea_prepare(...)
   3.     └─bugsigdbr::importBugSigDB()
   4.       └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
   5.         ├─base::suppressWarnings(...)
   6.         │ └─base::withCallingHandlers(...)
   7.         ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
   8.         └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
   9.           └─BiocFileCache:::.util_download_and_rename(...)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 39 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘FAQs.Rmd’ using rmarkdown
--- finished re-building ‘FAQs.Rmd’

--- re-building ‘ORA_vs_ES.Rmd’ using rmarkdown
--- finished re-building ‘ORA_vs_ES.Rmd’

--- re-building ‘TaxSEA.Rmd’ using rmarkdown

Quitting from TaxSEA.Rmd:138-151 [example2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
    ▆
 1. └─TaxSEA::TaxSEA(taxon_ranks = TaxSEA_test_data)
 2.   └─TaxSEA:::taxsea_prepare(...)
 3.     └─bugsigdbr::importBugSigDB()
 4.       └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 5.         ├─base::suppressWarnings(...)
 6.         │ └─base::withCallingHandlers(...)
 7.         ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 8.         └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 9.           └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TaxSEA.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘TaxSEA.Rmd’

--- re-building ‘Taxonomic-aggregation.Rmd’ using rmarkdown
--- finished re-building ‘Taxonomic-aggregation.Rmd’

--- re-building ‘single-sample-enrichment.Rmd’ using rmarkdown
--- finished re-building ‘single-sample-enrichment.Rmd’

--- re-building ‘why-taxon-set-enrichment.Rmd’ using rmarkdown
--- finished re-building ‘why-taxon-set-enrichment.Rmd’

SUMMARY: processing the following file failed:
  ‘TaxSEA.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/TaxSEA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL TaxSEA
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘TaxSEA’ ...
** this is package ‘TaxSEA’ version ‘1.5.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Error while performing HEAD request.
   Proceeding without cache information.
Saving _problems/test-TaxSEA-3.R
Detected SummarizedExperiment input. Extracting taxonomy from rowData().
Using mia::taxonomyRanks() to identify rank columns: Kingdom, Phylum, Class, Order, Family, Genus, Species
Detected SummarizedExperiment input. Extracting taxonomy from rowData().
Using mia::taxonomyRanks() to identify rank columns: Phylum, Genus, Species
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 39 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-TaxSEA.R:3:3'): TaxSEA returns valid output with test data ─────
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─TaxSEA::TaxSEA(TaxSEA_test_data) at test-TaxSEA.R:3:3
 2.   └─TaxSEA:::taxsea_prepare(...)
 3.     └─bugsigdbr::importBugSigDB()
 4.       └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 5.         ├─base::suppressWarnings(...)
 6.         │ └─base::withCallingHandlers(...)
 7.         ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 8.         └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 9.           └─BiocFileCache:::.util_download_and_rename(...)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 39 ]
Error:
! Test failures.
Execution halted