##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BiocPkgTools_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocPkgTools.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: 2026-05-22 02:02:29 UTC
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.30.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
pkgCombDependencyGain 18.022  0.770  27.790
get_bioc_data         16.193  0.465  17.046
firstInBioc           14.831  0.408  15.618
biocDownloadStats     13.185  0.555  28.173
pkgDepMetrics         12.935  0.441  22.076
biocBuildReport        7.260  2.448 233.742
inducedSubgraphByPkgs  8.359  0.445  84.296
biocMaintained         6.556  0.183   6.849
class-dependencies     5.305  0.203   5.509
biocRevDepEmail        3.850  0.229 979.618
pkgDownloadRank        2.138  0.106  12.813
pkgDownloadStats       0.096  0.012  75.125
* 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. └─BiocPkgTools::biocBuildReport("3.12") at test_biocBuildReport.R:8:5
    2.   ├─xml2::read_html(url)
    3.   └─xml2:::read_html.default(url)
    4.     ├─base::suppressWarnings(...)
    5.     │ └─base::withCallingHandlers(...)
    6.     ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
    7.     └─xml2:::read_xml.character(...)
    8.       └─xml2:::read_xml.connection(...)
    9.         ├─base::open(x, "rb")
   10.         └─base::open.connection(x, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 40 ]
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.30.0’
** 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 4.6.0 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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
Saving _problems/test_biocBuildReport-8.R
trying URL 'https://bioconductor.org/packages/3.23/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1397706 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 40 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_biocBuildReport.R:8:5'): columns are consistent in report output ──
Error in `open.connection(x, "rb")`: cannot open the connection
Backtrace:
     ▆
  1. └─BiocPkgTools::biocBuildReport("3.12") at test_biocBuildReport.R:8:5
  2.   ├─xml2::read_html(url)
  3.   └─xml2:::read_html.default(url)
  4.     ├─base::suppressWarnings(...)
  5.     │ └─base::withCallingHandlers(...)
  6.     ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  7.     └─xml2:::read_xml.character(...)
  8.       └─xml2:::read_xml.connection(...)
  9.         ├─base::open(x, "rb")
 10.         └─base::open.connection(x, "rb")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 40 ]
Error:
! Test failures.
Execution halted