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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 (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ... ERROR
Running examples in ‘DspikeIn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_spike_percentage
> ### Title: Calculate Spike Percentage for Specified Taxa in a Phyloseq or
> ###   TSE Object
> ### Aliases: calculate_spike_percentage
> 
> ### ** Examples
> 
> if (requireNamespace("DspikeIn", quietly = TRUE)) {
+   # Load example phyloseq object
+   data("physeq_16SOTU", package = "DspikeIn")
+ 
+   # ----------- Phyloseq Example -----------
+   species_name <- c("Tetragenococcus_halophilus", "Tetragenococcus_sp.")
+   merged_spiked_species <- "Tetragenococcus_halophilus"
+ 
+   # Pre-process the phyloseq object to merge spike-in taxa
+   merged_physeq <- Pre_processing_species(
+     physeq_16SOTU,
+     species_name = species_name,
+     merge_method = "sum"
+   )
+ 
+   # Perform spike-in percentage calculation
+   output_docx <- file.path(tempdir(), "spike_summary_physeq.docx")
+   result_physeq <- calculate_spike_percentage(
+     obj = merged_physeq,
+     merged_spiked_species = merged_spiked_species,
+     output_file = output_docx,
+     passed_range = c(0.1, 20)
+   )
+   print(result_physeq)
+ 
+   # ----------- TSE Example -----------
+   tse_16SOTU <- convert_phyloseq_to_tse(physeq_16SOTU)
+   merged_tse <- Pre_processing_species(
+     tse_16SOTU,
+     species_name = species_name,
+     merge_method = "sum"
+   )
+ 
+   output_docx_tse <- file.path(tempdir(), "spike_summary_tse.docx")
+   result_tse <- calculate_spike_percentage(
+     obj = merged_tse,
+     merged_spiked_species = merged_spiked_species,
+     output_file = output_docx_tse,
+     passed_range = c(0.1, 20)
+   )
+   print(result_tse)
+ 
+   # Clean up temporary files
+   if (file.exists(output_docx)) unlink(output_docx, force = TRUE)
+   if (file.exists(output_docx_tse)) unlink(output_docx_tse, force = TRUE)
+ }
Starting pre-processing...
Checking taxonomy table...
Processing taxon: Tetragenococcus_halophilus
Single ASV found for: Tetragenococcus_halophilus. No merging needed.
Processing taxon: Tetragenococcus_sp.
Merging 16 ASVs for: Tetragenococcus_sp.
Merging completed for: Tetragenococcus_sp.
Pruned phylogenetic tree to match taxa.
Pruned reference sequences to match taxa.
Pre-processing complete.
Error in xml_find_all.xml_node(header$get(), "//a:blip[contains(@r:embed, 'rId')]") : 
  xmlXPathEval: evaluation failed
Calls: calculate_spike_percentage ... <Anonymous> -> print -> print.rdocx -> sanitize_images
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
RandomForest_selected     42.365  1.152  47.086
Pre_processing_hashcodes  13.219  0.435  15.002
alluvial_plot              6.706  0.277   7.402
calculate_spikeIn_factors  6.540  0.196   7.139
Pre_processing_species     6.225  0.172   6.972
* 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 ERROR, 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-x86_64/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 (2025-11-05 r88990) -- "[Not] Part in a Rumble"
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.

> # 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 
 26.971   1.608  30.415