===============================
R CMD BUILD
===============================
* checking for file ‘DspikeIn/DESCRIPTION’ ... OK
* preparing ‘DspikeIn’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘DspikeIn_0.99.28.tar.gz’
===============================
BiocCheckGitClone('DspikeIn')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/155b0b3c100494a2fb36b06d8e05c78d51e5f2da/DspikeIn
→ BiocVersion: 3.22
→ Package: DspikeIn
→ PackageVersion: 0.99.28
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/155b0b3c100494a2fb36b06d8e05c78d51e5f2da/DspikeIn.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/155b0b3c100494a2fb36b06d8e05c78d51e5f2da/DspikeIn
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3778/155b0b3c100494a2fb36b06d8e05c78d51e5f2da/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
* using option ‘--no-vignettes’
* checking for file ‘DspikeIn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DspikeIn’ version ‘0.99.28’
* 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 for future file timestamps ... 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking whether startup messages can be suppressed ... [11s/11s] OK
* checking use of S3 registration ... 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 ... [40s/40s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 ... [10s/10s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [284s/283s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
perform_and_visualize_DA 51.049 0.227 51.281
taxa_barplot 35.699 0.243 35.945
plot_core_microbiome_custom 19.854 0.126 19.982
RandomForest_selected 16.459 0.307 16.767
summ_ASV_OTUID 13.905 0.000 13.906
node_level_metrics 9.614 0.034 9.522
convert_to_absolute_counts 8.031 0.130 8.162
calculate_spike_percentage 7.208 0.118 7.099
Pre_processing_hashcodes 6.303 0.240 6.547
quadrant_plot 6.264 0.020 6.127
ridge_plot_it 5.233 0.001 5.235
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/11s]
[11s/11s] 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 ... [5s/5s] OK
* DONE
Status: OK
===============================
BiocCheck('DspikeIn_0.99.28.tar.gz')
===============================
── Installing DspikeIn ─────────────────────────────────────────────────────────
✔ Package installed successfully
── DspikeIn session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1HzPzu/file2611df3d5bbb29/DspikeIn
→ BiocVersion: 3.22
→ Package: DspikeIn
→ PackageVersion: 0.99.28
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/155b0b3c100494a2fb36b06d8e05c78d51e5f2da/DspikeIn.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/Rtmp1HzPzu/file2611df3d5bbb29/DspikeIn
→ installDir: /tmp/Rtmp1HzPzu/file2611df3431cdd0
→ 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 new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* 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 that Package field matches directory/tarball name...
* 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 whether vignette is built with 'R CMD build'...
* 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 184, column 32)
• R/perform_and_visualize_DA.R (line 200, 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 if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 17 NOTES
i See the DspikeIn.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.