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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiocPkgTools_1.21.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocPkgTools.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.21.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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_base’
  ‘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 ... NOTE
checkRd: (-1) githubURLParts.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) githubURLParts.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) githubURLParts.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) githubURLParts.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:31-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:47-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repositoryStats.Rd:61-66: Lost braces in \itemize; \value handles \item{}{} directly
* 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       29.361 13.186  33.097
get_bioc_data         11.725  0.863  13.423
firstInBioc           11.540  0.968  13.304
biocDownloadStats     11.221  0.547  12.668
pkgCombDependencyGain  8.127  0.464   8.833
pkgDepMetrics          6.846  0.404   7.456
class-dependencies     5.598  0.418   6.020
inducedSubgraphByPkgs  5.053  0.631   6.457
biocMaintained         3.974  0.240   5.650
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BiocPkgTools
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘BiocPkgTools’ ...
** 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) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 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/3.19/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1305972 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 30.689   3.870  33.992