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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_1.29.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BiocPkgTools.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 ‘1.29.2’
* 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 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        9.985 56.057  73.419
get_bioc_data         16.139  0.741  17.580
firstInBioc           15.288  0.705  16.677
biocDownloadStats     14.290  0.764  16.237
pkgCombDependencyGain 10.769  0.655  26.403
inducedSubgraphByPkgs  9.743  0.378  17.340
biocMaintained         8.054  0.562   8.900
pkgDepMetrics          6.955  0.326  21.673
class-dependencies     6.168  0.247   6.489
githubDetails          3.102  0.589   7.019
pkgDownloadRank        2.139  0.213   6.081
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-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/4.6-x86_64/Resources/library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.29.2’
** 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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")



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 0 | WARN 2 | SKIP 0 | PASS 37 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
 37.696  46.898 122.576