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### Running command:
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###   /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                         44.821  1.453  65.798
plot_core_microbiome_custom          29.097  0.844  41.870
RandomForest_selected                24.446  0.586  35.973
summ_ASV_OTUID                       16.589  0.343  24.027
convert_to_absolute_counts           13.995  0.474  20.564
node_level_metrics                   12.163  0.283  17.645
Pre_processing_hashcodes             12.160  0.252  16.911
calculate_spike_percentage           10.741  0.727  16.791
quadrant_plot                         7.889  0.172  11.442
random_subsample_WithReductionFactor  6.882  0.876  10.903
proportion_adj                        7.426  0.223  10.573
ridge_plot_it                         7.134  0.216  10.246
calculate_spikeIn_factors             6.648  0.287   9.796
Pre_processing_species                5.431  0.143   8.092
normalization_set                     4.917  0.425   7.538
summ_phyloseq_sampleID                4.009  0.937   6.999
alluvial_plot                         4.583  0.165   6.464
filter_and_split_abundance            4.168  0.087   5.855
weight_Network                        3.971  0.133   5.991
degree_network                        3.789  0.128   5.543
simulate_network_robustness           3.720  0.103   5.313
randomsubsample_Trimmed_evenDepth     3.524  0.213   5.198
* 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.