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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.16.1’
* 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 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 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
integration_alluvial_plot      6.717  0.097  19.222
sharing_venn                   4.981  0.245  72.638
import_parallel_Vispa2Matrices 2.937  0.211  24.697
CIS_grubbs_overtime            2.475  0.331  13.762
sharing_heatmap                2.283  0.054  18.291
import_Vispa2_stats            2.129  0.203  11.941
top_cis_overtime_heatmap       2.168  0.085  13.256
iss_source                     1.387  0.054  13.063
HSC_population_plot            1.359  0.030  11.941
is_sharing                     1.152  0.045  15.044
realign_after_collisions       1.063  0.036  10.541
remove_collisions              1.018  0.035  10.404
compute_near_integrations      0.887  0.033  18.509
HSC_population_size_estimate   0.885  0.029  11.503
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ISAnalytics
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/Rtmpo59CTS/file1450c6c6b8360/2025-03-07_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/Rtmpo59CTS/file1450c77f522e2/2025-03-07_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 834 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
185.378   7.350 519.685