##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DspikeIn.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DspikeIn_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DspikeIn.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DspikeIn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DspikeIn’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 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 ‘DspikeIn’ 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'label.Rd':
  ‘[phyloseq:tax_table-methods]{phyloseq::tax_table()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... 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
taxa_barplot                         43.580  1.359  62.471
plot_core_microbiome_custom          28.788  0.850  41.743
RandomForest_selected                24.281  0.635  34.667
convert_to_absolute_counts           16.895  0.507  24.383
summ_ASV_OTUID                       16.354  0.332  22.836
Pre_processing_hashcodes             13.308  0.227  18.716
node_level_metrics                   12.323  0.294  17.766
calculate_spike_percentage           11.407  0.787  17.326
random_subsample_WithReductionFactor  6.844  1.024  11.092
quadrant_plot                         7.727  0.101  11.054
proportion_adj                        7.509  0.227  10.757
ridge_plot_it                         7.268  0.224  10.455
summ_phyloseq_sampleID                5.537  0.984   8.978
alluvial_plot                         6.048  0.228   8.948
Pre_processing_species                5.787  0.143   8.418
calculate_spikeIn_factors             5.255  0.194   7.786
filter_and_split_abundance            5.296  0.132   7.732
normalization_set                     4.829  0.439   7.694
simulate_network_robustness           3.677  0.102   5.358
* 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-3.22-bioc/meat/DspikeIn.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DspikeIn
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘DspikeIn’ ...
** this is package ‘DspikeIn’ version ‘1.0.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (DspikeIn)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # 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(DspikeIn)

Thank you for using DspikeIn! 🎉
For support, 📧 contact: Mitra Ghotbi (mitra.ghotbi@gmail.com)
GitHub Repository: https://github.com/mghotbi/DspikeIn
🐛 Found a bug or have a suggestion? Open an issue:
  https://github.com/mghotbi/DspikeIn/issues


> 
> test_check("DspikeIn")
[ FAIL 0 | WARN 0 | SKIP 13 | PASS 0 ]

══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On Bioconductor (13): 'test-Pre_processing_species.R:1:1',
  'test-RandomForest_selected.R:1:1', 'test-calculate_spikeIn_factors.R:1:1',
  'test-calculate_spike_percentage.R:1:1',
  'test-calculate_summary_stats_table.R:1:1', 'test-conclusion.R:1:1',
  'test-convert_to_absolute_counts.R:1:1',
  'test-imbalance_calculate_list_average_scaling_factors.R:1:1',
  'test-node_level_metrics.R:1:1', 'test-perform_and_visualize_DA.R:1:1',
  'test-quadrant_plot.R:1:1', 'test-remove_zero_negative_count_samples.R:1:1',
  'test-simulate_robustness.R:1:1'

[ FAIL 0 | WARN 0 | SKIP 13 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 15.760   0.757  23.118