##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CTexploreR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CTexploreR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CTexploreR/DESCRIPTION’ ... OK
* this is package ‘CTexploreR’ version ‘1.2.0’
* 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 ‘CTexploreR’ 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
DAC_induction                    9.102  0.408  11.963
embryos_mean_methylation         9.036  0.409  11.138
normal_tissues_methylation       7.023  0.707   9.348
fetal_germcells_mean_methylation 5.418  0.302   6.853
normal_tissues_mean_methylation  5.232  0.191   7.101
HPA_cell_type_expression         3.779  0.265   6.406
GTEX_expression                  3.770  0.121   5.286
* 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-3.20-bioc/R/bin/R CMD INSTALL CTexploreR
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘CTexploreR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
see ?CTdata and browseVignettes('CTdata') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
** 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 (CTexploreR)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(CTexploreR)
Loading required package: CTdata
> 
> test_check("CTexploreR")
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 135 ]
Deleting unused snapshots:
• GTEX_expression/gtex-expression-on-mage.svg
> 
> proc.time()
    user   system  elapsed 
 981.153   69.447 1218.376