##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:annotatr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings annotatr_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/annotatr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.34.0’
* 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 ‘annotatr’ 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 ... NOTE
plot_coannotations: no visible binding for global variable ‘.’
plot_numerical_coannotations: no visible binding for global variable
  ‘.’
Undefined global functions or variables:
  .
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
build_annotations 4.972  0.464   5.436
build_ah_annots   3.827  0.695   5.497
* 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:
  dplyr::setequal(class(dm_vs_num_co2), c("gg", "ggplot")) not equal to TRUE.
  1 element mismatch
  ── Failure ('test_7_visualize.R:290:5'): Test plot_categorical() success ───────
  dplyr::setequal(class(dm_vn_min), c("gg", "ggplot")) not equal to TRUE.
  1 element mismatch
  ── Failure ('test_7_visualize.R:291:5'): Test plot_categorical() success ───────
  dplyr::setequal(class(dm_vn), c("gg", "ggplot")) not equal to TRUE.
  1 element mismatch
  ── Failure ('test_7_visualize.R:292:5'): Test plot_categorical() success ───────
  dplyr::setequal(class(dm_vn_rnd), c("gg", "ggplot")) not equal to TRUE.
  1 element mismatch
  
  [ FAIL 12 | WARN 4 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/annotatr.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL annotatr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘annotatr’ ...
** this is package ‘annotatr’ version ‘1.34.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (annotatr)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
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(annotatr)
> 
> test_check("annotatr")
[ FAIL 12 | WARN 4 | SKIP 0 | PASS 60 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_7_visualize.R:80:5'): Test plot_annotation() success ─────────
dplyr::setequal(class(dm_va_min), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:81:5'): Test plot_annotation() success ─────────
dplyr::setequal(class(dm_va), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:82:5'): Test plot_annotation() success ─────────
dplyr::setequal(class(dm_va_rnd), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:96:5'): Test plot_coannotations() success ──────
dplyr::setequal(class(dm_vs_ca), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:154:5'): Test plot_numerical() success ─────────
dplyr::setequal(class(dm_vs_regions_mu1), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:155:5'): Test plot_numerical() success ─────────
dplyr::setequal(class(dm_vs_regions_annot), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:156:5'): Test plot_numerical() success ─────────
dplyr::setequal(class(dm_vs_regions_name), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:185:5'): Test plot_numerical_coannotations() ───
dplyr::setequal(class(dm_vs_num_co1), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:186:5'): Test plot_numerical_coannotations() ───
dplyr::setequal(class(dm_vs_num_co2), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:290:5'): Test plot_categorical() success ───────
dplyr::setequal(class(dm_vn_min), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:291:5'): Test plot_categorical() success ───────
dplyr::setequal(class(dm_vn), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch
── Failure ('test_7_visualize.R:292:5'): Test plot_categorical() success ───────
dplyr::setequal(class(dm_vn_rnd), c("gg", "ggplot")) not equal to TRUE.
1 element mismatch

[ FAIL 12 | WARN 4 | SKIP 0 | PASS 60 ]
Error: Test failures
Execution halted