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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tissueTreg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings tissueTreg_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/tissueTreg.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘tissueTreg/DESCRIPTION’ ... OK
* this is package ‘tissueTreg’ version ‘1.20.0’
* 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 ‘tissueTreg’ 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 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 Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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
tissueTreg 9.332   0.56   10.32
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tissueTreg.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘tissueTreg.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-data-experiment/meat/tissueTreg.Rcheck/vign_test/tissueTreg/vignettes/tissueTreg_files/figure-html/plotRegion-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-data-experiment/meat/tissueTreg.Rcheck/vign_test/tissueTreg/vignettes/tissueTreg_files/figure-html/plotRegionColor-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-data-experiment/meat/tissueTreg.Rcheck/vign_test/tissueTreg/vignettes/tissueTreg_files/figure-html/plotRegionColor_group-1.png" but not available.

Quitting from lines 146-157 [RNA-seq_foxp3_vis] (tissueTreg.Rmd)
Error: processing vignette 'tissueTreg.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘tissueTreg.Rmd’

SUMMARY: processing the following file failed:
  ‘tissueTreg.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-data-experiment/meat/tissueTreg.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tissueTreg
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘tissueTreg’ ...
** using staged installation
** inst
** 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 (tissueTreg)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(tissueTreg)
> 
> test_check("tissueTreg")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 16.979   0.966  18.622