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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DspikeIn_1.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DspikeIn ─────────────────────────────────────────────────────────
✔ Package installed successfully
── DspikeIn session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9rzLAm/file85781169cba04/DspikeIn
→ BiocVersion: 3.24
→ Package: DspikeIn
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DspikeIn.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp9rzLAm/file85781169cba04/DspikeIn
→ installDir: /tmp/Rtmp9rzLAm/file857815e90208b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DspikeIn ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Classification
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (30%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DspikeIn-with-TSE.Rmd
* Checking package installation calls in R code...
* Checking for library/require of DspikeIn...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/perform_and_visualize_DA.R (line 185, column 32)
    • R/perform_and_visualize_DA.R (line 201, column 29)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/imbalance_calculate_list_average_scaling_factors.R (line 194,
    column 7)
    • ...
    • print() in R/RandomForest_selected.R (line 174, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/plotbar_abundance.R (line 91, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/alluvial_plot.R (line 90, column 10)
    • ...
    • R/weight_Network.R (line 58, column 40)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 37
functions greater than 50 lines.
  The longest 5 functions are:
    • perform_and_visualize_DA() (R/perform_and_visualize_DA.R): 428 lines
    • ...
    • alluvial_plot() (R/alluvial_plot.R): 171 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • detect_common_asvs_taxa.Rd
  • ...
  • plotbar_abundance.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 6% of man
pages use at least one of these tags.
  Found in files:
    • alluvial_plot.Rd
    • ...
    • plotbar_abundance.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • detect_common_asvs_taxa.Rd
    • plot_spikein_tree_diagnostic.Rd
    • plotbar_abundance.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files:
test-calculate_spike_percentage.R test-calculate_spikeIn_factors.R
test-calculate_summary_stats_table.R test-conclusion.R
test-convert_to_absolute_counts.R
test-imbalance_calculate_list_average_scaling_factors.R
test-node_level_metrics.R test-perform_and_visualize_DA.R
test-Pre_processing_species.R test-quadrant_plot.R test-RandomForest_selected.R
test-remove_zero_negative_count_samples.R test-simulate_robustness.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 1030 lines (10%) are > 80 characters long.
  First few lines:
    • R/aaa-ExpData_class.R#L2 #' @description This is a virtual superc ...
    • ...
    • vignettes/DspikeIn-with-TSE.Rmd#L1585 Quantitative PCR (qPCR) was used to
    comp ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • vignettes/DspikeIn-with-TSE.Rmd#L192 Tip labels= OTU/ASV names ...
    • ...
    • vignettes/DspikeIn-with-TSE.Rmd#L213 # Branch length numbers= Actual
    evolutio ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2677 lines (26%) are
not.
  First few lines:
    • R/accessors.R#L11 if (inherits(obj, "phyloseq")) { ...
    • ...
    • vignettes/DspikeIn-with-TSE.Rmd#L1574 if (dir.exists(folder))
    unlink(folder, ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 18 NOTES
ℹ See the DspikeIn.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.