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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocPkgTools_1.27.12.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.27.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘BiocPkgTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocManager:::.repositories’ ‘BiocManager:::.repositories_bioc’
  ‘BiocManager:::.repository_container_version’
  ‘BiocManager:::.version_bioc’
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
biocBuildReport       12.670  6.127  25.656
biocDownloadStats     17.807  0.882  26.869
get_bioc_data         16.299  1.093  21.398
firstInBioc           16.004  1.032  19.991
pkgCombDependencyGain 11.783  0.650  21.465
class-dependencies     7.869  0.410   9.335
pkgDepMetrics          7.362  0.502  17.053
inducedSubgraphByPkgs  6.274  0.514   8.402
biocMaintained         5.242  0.194   7.422
biocRevDepEmail        2.941  0.100   5.364
* 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:
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 18 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_biocBuildReport.R:8:5'): columns are consistent in report output ──
  Error in `do.call(rbind, unlist(url_list, recursive = FALSE))`: second argument must be a list
  Backtrace:
      ▆
   1. └─BiocPkgTools::biocBuildReport("3.12") at test_biocBuildReport.R:8:5
   2.   └─BiocPkgTools::biocBuildStatusDB(version, pkgType)
   3.     └─base::do.call(rbind, unlist(url_list, recursive = FALSE))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BiocPkgTools
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.27.12’
** using staged installation
** R
** 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 (BiocPkgTools)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.21/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1397541 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 18 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_biocBuildReport.R:8:5'): columns are consistent in report output ──
Error in `do.call(rbind, unlist(url_list, recursive = FALSE))`: second argument must be a list
Backtrace:
    ▆
 1. └─BiocPkgTools::biocBuildReport("3.12") at test_biocBuildReport.R:8:5
 2.   └─BiocPkgTools::biocBuildStatusDB(version, pkgType)
 3.     └─base::do.call(rbind, unlist(url_list, recursive = FALSE))

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted