===============================
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_0.99.10.tar.gz’
===============================
BiocCheckGitClone('DspikeIn')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/0b7785bec182dbc45830b3adc05d2a6cb27226e8/DspikeIn
→ BiocVersion: 3.22
→ Package: DspikeIn
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/0b7785bec182dbc45830b3adc05d2a6cb27226e8/DspikeIn.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/0b7785bec182dbc45830b3adc05d2a6cb27226e8/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 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 v1.45.7 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/3778/0b7785bec182dbc45830b3adc05d2a6cb27226e8/DspikeIn.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 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 ‘0.99.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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 ... [10s/10s] 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 ... [35s/35s] 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 ... [265s/265s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normalization_set 153.564 1.158 154.734
calculate_summary_stats_table 21.128 0.348 21.338
summ_ASV_OTUID 13.878 0.041 13.920
convert_to_absolute_counts 8.551 0.071 8.624
calculate_spike_percentage 8.016 0.303 8.089
calculate_spikeIn_factors 5.453 0.029 5.482
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [25s/25s]
[25s/25s] 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 ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('DspikeIn_0.99.10.tar.gz')
===============================
── Installing DspikeIn ─────────────────────────────────────────────────────────
✔ Package installed successfully
── DspikeIn session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNLnXby/file3e347c3dbc4b6e/DspikeIn
→ BiocVersion: 3.22
→ Package: DspikeIn
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3778/0b7785bec182dbc45830b3adc05d2a6cb27226e8/DspikeIn.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpNLnXby/file3e347c3dbc4b6e/DspikeIn
→ installDir: /tmp/RtmpNLnXby/file3e347c51cebbf0
→ 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 (36%).
* 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• Getting-started-with-DspikeIn.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 redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/calculate_spikeIn_factors.R (line 102, column 48)
• ...
• R/summ_phyloseq_sampleID.R (line 42, column 10)
* 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 18
functions greater than 50 lines.
The longest 5 functions are:
• validate_spikein_clade() (R/validate_spikein_clade.R): 198 lines
• ...
• norm.rle() (R/normalization_set.R): 125 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• get_otu_table.Rd
• ...
• plot_spikein_tree_diagnostic.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
Found in files:
• plot_spikein_tree_diagnostic.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• plot_spikein_tree_diagnostic.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 467 lines (8%) are > 80 characters long.
First few lines:
• R/aaa-ExpData_class.R#L2 #' @description This is a virtual superc ...
• ...
• vignettes/Getting-started-with-DspikeIn.Rmd#L813 Quantitative PCR (qPCR) was
used to comp ...
i NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
First few lines:
• vignettes/Getting-started-with-DspikeIn.Rmd#L318 Tip labels= OTU/ASV names
...
• ...
• vignettes/Getting-started-with-DspikeIn.Rmd#L338 # Branch length numbers=
Actual evolutio ...
i NOTE: Consider multiples of 4 spaces for line indents; 1391 lines (25%) are
not.
First few lines:
• R/accessors.R#L11 if (inherits(obj, "phyloseq")) { ...
• ...
• vignettes/Getting-started-with-DspikeIn.Rmd#L802 } ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 13 NOTES
i See the DspikeIn.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.