##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gDRstyle.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gDRstyle_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gDRstyle.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘gDRstyle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRstyle’ version ‘1.7.2’
* 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 ‘gDRstyle’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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
checkPackage 10.84  2.519  15.938
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL gDRstyle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘gDRstyle’ ...
** this is package ‘gDRstyle’ version ‘1.7.2’
** 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 (gDRstyle)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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(gDRstyle)
> 
> test_check("gDRstyle")
##------ Wed Jun 18 23:22:09 2025 ------##
##------ Wed Jun 18 23:22:09 2025 ------##
✔ | F W  S  OK | Context

⠏ |          0 | pkg                                                            
✔ |          1 | pkg

══ Results ═════════════════════════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
── Initialising site ───────────────────────────────────────────────────────────
Copying <pkgdown>/BS3/assets/bootstrap-toc.css to bootstrap-toc.css
Copying <pkgdown>/BS3/assets/bootstrap-toc.js to bootstrap-toc.js
Copying <pkgdown>/BS3/assets/docsearch.css to docsearch.css
Copying <pkgdown>/BS3/assets/docsearch.js to docsearch.js
Copying <pkgdown>/BS3/assets/link.svg to link.svg
Copying <pkgdown>/BS3/assets/pkgdown.css to pkgdown.css
Copying <pkgdown>/BS3/assets/pkgdown.js to pkgdown.js
── Building pkgdown site for package fakePkg ───────────────────────────────────
Reading from:
/home/biocbuild/bbs-3.22-bioc/R/site-library/gDRstyle/tst_pkgs/dummy_pkg
Writing to: /tmp/RtmpGikSk6/file10c32021d1c0c
── Sitrep ──────────────────────────────────────────────────────────────────────
✖ Bootstrap 3 is deprecated; please switch to Bootstrap 5.
ℹ Learn more at
  <https://www.tidyverse.org/blog/2021/12/pkgdown-2-0-0/#bootstrap-5>.
✖ URLs not ok.
  In _pkgdown.yml, url is missing.
  See details in `vignette(pkgdown::metadata)`.
✔ Favicons ok.
✔ Open graph metadata ok.
✔ Articles metadata ok.
✔ Reference metadata ok.
── Initialising site ───────────────────────────────────────────────────────────
── Building home ───────────────────────────────────────────────────────────────
Writing `authors.html`
Reading 'DESCRIPTION'
Writing `index.html`
Writing `404.html`
── Building function reference ─────────────────────────────────────────────────
Writing `reference/index.html`
Reading man/tstCharLimitLintr.Rd
Writing `reference/tstCharLimitLintr.html`
── Building sitemap ────────────────────────────────────────────────────────────
Writing `sitemap.xml`
── Checking for problems ───────────────────────────────────────────────────────
── Finished building pkgdown site for package fakePkg ──────────────────────────
##------ Wed Jun 18 23:22:13 2025 ------##
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘fakePkg’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘fakePkg_1.0.tar.gz’

── R CMD check ─────────────────────────────────────────────────────────────────
* using log directory ‘/tmp/RtmpGikSk6/file10c32063a60a0b/fakePkg.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-tests --no-manual’
* checking for file ‘fakePkg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fakePkg’ version ‘1.0’
* 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 ‘fakePkg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  What license is it under?
Standardizable: FALSE
* 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 ... OK
* 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 examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... SKIPPED
* DONE

Status: 1 NOTE
See
  ‘/tmp/RtmpGikSk6/file10c32063a60a0b/fakePkg.Rcheck/00check.log’
for details.
##------ Wed Jun 18 23:22:25 2025 ------##
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 24 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-dependencies.R:16:1'
• skip, if there is installed fakePkg (1): 'test-build.R:53:3'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
 12.208   2.654  17.386