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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings BiocPkgTools_1.29.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocPkgTools.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 ‘1.29.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Sean Davis <seandavi@gmail.com>’

License components with restrictions and base license permitting such:
  MIT + file LICENSE
File 'LICENSE':
  MIT License
  
  Copyright (c) 2018 Sean Davis
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in all
  copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Title field should be in title case. Current version is:
  ‘Collection of simple tools for learning about Bioconductor Packages’
In title case that is:
  ‘Collection of Simple Tools for Learning About Bioconductor Packages’

The BugReports field in DESCRIPTION has
  https://github.com/seandavi/BiocPkgTools/issues/new
which should likely be
  https://github.com/seandavi/BiocPkgTools/issues/new/issues
instead.
* 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 use of S3 registration ... 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 ... ERROR
Running examples in ‘BiocPkgTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biocRevDepEmail
> ### Title: Notify downstream maintainers of changes in upstream packages
> ### Aliases: biocRevDepEmail
> 
> ### ** Examples
> 
> 
> biocRevDepEmail(
+     "FindMyFriends", version = "3.13", dry.run = TRUE, textOnly = TRUE
+ )
Error in biocPkgList(version = version) : 
  'version' is not 'release', 'devel', or a valid 'package_version'
Calls: biocRevDepEmail -> biocPkgList
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
biocBuildReport   6.254  5.163   8.947
biocDownloadStats 8.110  0.264   8.861
* 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:
  downloaded 1.3 MB
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_biocBuildReport.R:8:5'): columns are consistent in report output ──
  Error in `biocBuildReport("3.12")`: 'version' is not 'release', 'devel', or a valid 'package_version'
  Backtrace:
      ▆
   1. └─BiocPkgTools::biocBuildReport("3.12") at test_biocBuildReport.R:8:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  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: 2 ERRORs, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocPkgTools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.29.1’
** 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 Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
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")
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 1397976 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_biocBuildReport.R:8:5'): columns are consistent in report output ──
Error in `biocBuildReport("3.12")`: 'version' is not 'release', 'devel', or a valid 'package_version'
Backtrace:
    ▆
 1. └─BiocPkgTools::biocBuildReport("3.12") at test_biocBuildReport.R:8:5

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
Error:
! Test failures.
Execution halted