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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.28.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.28.1’
* 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 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
+ )
Provide your full name: 
What is your core-team email? 
What is your employee ID (e.g., AB12345, leave blank if N/A)? 
Saved data to: /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocPkgTools
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   11.841 40.815  71.599
biocDownloadStats 16.480  0.579  22.281
biocMaintained     7.999  0.403  10.453
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocPkgTools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.28.1’
** 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 version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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/3.22/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1397833 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