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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ISAnalytics_1.11.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.11.1’
* 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 ‘ISAnalytics’ 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 R 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 startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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
integration_alluvial_plot      4.175  0.183  11.232
sharing_venn                   3.480  0.358  47.683
import_parallel_Vispa2Matrices 2.550  0.841  16.144
import_Vispa2_stats            1.612  0.207   7.305
sharing_heatmap                1.625  0.167  11.277
CIS_grubbs_overtime            1.602  0.175   8.118
top_cis_overtime_heatmap       1.662  0.053   8.142
iss_source                     1.073  0.184   8.162
HSC_population_plot            1.020  0.140   7.379
remove_collisions              0.911  0.103   6.721
is_sharing                     0.939  0.044   8.966
realign_after_collisions       0.896  0.081   6.617
compute_near_integrations      0.625  0.038  11.592
HSC_population_size_estimate   0.638  0.018   6.841
* 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 ...
  ‘ISAnalytics.Rmd’ using ‘UTF-8’... OK
  ‘workflow_start.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ISAnalytics
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘ISAnalytics’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ISAnalytics)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(ISAnalytics)
> 
> test_check("ISAnalytics")
Loading required namespace: plotly
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: /tmp/RtmpiZsa2z/file3bdfb128536d7d/2023-06-06_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpiZsa2z/file3bdfb14decc15b/2023-06-06_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 833 ]
> 
> proc.time()
   user  system elapsed 
122.399   4.903 316.632