##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DspikeIn.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DspikeIn_0.99.29.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DspikeIn.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘DspikeIn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DspikeIn’ version ‘0.99.29’
* 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 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 ... 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                36.957  0.177  37.135
plot_core_microbiome_custom 22.610  0.061  22.671
RandomForest_selected       18.536  0.224  18.759
summ_ASV_OTUID              16.148  0.053  16.202
node_level_metrics          10.405  0.042  10.360
convert_to_absolute_counts   9.917  0.160  10.095
calculate_spike_percentage   8.377  0.140   8.283
Pre_processing_hashcodes     7.194  0.390   7.590
quadrant_plot                6.808  0.027   6.764
ridge_plot_it                5.664  0.058   5.723
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DspikeIn.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DspikeIn
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘DspikeIn’ ...
** this is package ‘DspikeIn’ version ‘0.99.29’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(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 
 12.261   0.613  12.861