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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ISAnalytics_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ISAnalytics.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘bslib::show_toast’ by ‘shinyWidgets::show_toast’ when loading ‘ISAnalytics’
See ‘/home/biocbuild/bbs-3.23-bioc/meat/ISAnalytics.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
* 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 whether 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 ... NOTE
checkRd: (-1) refGenes_hg19.Rd:21: Lost braces; missing escapes or markup?
    21 | \item Download from {http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/}
       |                     ^
* 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
sharing_venn                   4.602  0.346  34.374
integration_alluvial_plot      3.795  0.263  10.611
import_parallel_Vispa2Matrices 2.885  0.255  16.055
sharing_heatmap                2.078  0.148  10.537
top_cis_overtime_heatmap       1.777  0.094   8.229
import_Vispa2_stats            1.610  0.212   7.783
CIS_grubbs_overtime            1.662  0.156   7.269
iss_source                     1.538  0.081   8.230
is_sharing                     1.377  0.149   9.018
realign_after_collisions       1.189  0.079   6.938
remove_collisions              1.214  0.052   7.083
compute_near_integrations      0.911  0.017   5.796
HSC_population_size_estimate   0.905  0.009   5.768
* 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:
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 832 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-population-size-estimate.R:605:5'): .re_agg_and_estimate works as expected - less tps ──
  Error: Invalid index: out of bounds
  Backtrace:
      ▆
   1. └─ISAnalytics:::.re_agg_and_estimate(...) at test-population-size-estimate.R:605:5
   2.   ├─groups_dfs[[i]]
   3.   └─vctrs:::`[[.vctrs_list_of`(groups_dfs, i)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 832 ]
  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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ISAnalytics
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ISAnalytics’ ...
** this is package ‘ISAnalytics’ version ‘1.21.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘bslib::show_toast’ by ‘shinyWidgets::show_toast’ when loading ‘ISAnalytics’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘bslib::show_toast’ by ‘shinyWidgets::show_toast’ when loading ‘ISAnalytics’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘bslib::show_toast’ by ‘shinyWidgets::show_toast’ when loading ‘ISAnalytics’
** testing if installed package keeps a record of temporary installation path
* DONE (ISAnalytics)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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(ISAnalytics)
Warning message:
replacing previous import 'bslib::show_toast' by 'shinyWidgets::show_toast' when loading 'ISAnalytics' 
> 
> test_check("ISAnalytics")
Loading required namespace: plotly
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: /tmp/RtmpRRMHhe/file1dcddf1cbe2891/2026-02-10_collision_removal_report.html
Saving _problems/test-population-size-estimate-631.R
Report correctly saved
i Report saved to: /tmp/RtmpRRMHhe/file1dcddf59836514/2026-02-10_outlier_test_pool_fragments_report.html
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 832 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-population-size-estimate.R:605:5'): .re_agg_and_estimate works as expected - less tps ──
Error: Invalid index: out of bounds
Backtrace:
    ▆
 1. └─ISAnalytics:::.re_agg_and_estimate(...) at test-population-size-estimate.R:605:5
 2.   ├─groups_dfs[[i]]
 3.   └─vctrs:::`[[.vctrs_list_of`(groups_dfs, i)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 832 ]
Error:
! Test failures.
Execution halted