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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --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) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.21.8’
* 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             15.680 41.194 144.800
firstInBioc                 14.203  0.140  17.088
get_bioc_data               13.972  0.282  17.943
biocDownloadStats           12.438  0.455  27.998
pkgCombDependencyGain        8.245  0.125  18.233
pkgDepMetrics                7.688  0.194  14.318
class-dependencies           7.234  0.148   7.417
inducedSubgraphByPkgs        5.635  0.171   9.631
biocMaintained               3.983  0.172  12.166
buildPkgDependencyDataFrame  2.782  0.129   7.241
anacondaDownloadStats        1.940  0.784  78.351
biocRevDepEmail              2.290  0.035  18.793
pkgDownloadRank              2.022  0.043   8.139
biocPkgList                  1.330  0.048   6.464
getBiocVignette              1.211  0.019   5.393
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL BiocPkgTools
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 31.985   4.131  50.103