===============================
R CMD BUILD
===============================
* checking for file ‘wompwomp/DESCRIPTION’ ... OK
* preparing ‘wompwomp’:
* 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 ‘wompwomp_0.99.8.tar.gz’
===============================
BiocCheckGitClone('wompwomp')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/a59395ce07729b7c2a994d71277d78249fb863b9/wompwomp
→ BiocVersion: 3.22
→ Package: wompwomp
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/a59395ce07729b7c2a994d71277d78249fb863b9/wompwomp.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/a59395ce07729b7c2a994d71277d78249fb863b9/wompwomp
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3936/a59395ce07729b7c2a994d71277d78249fb863b9/wompwomp.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 ‘wompwomp/DESCRIPTION’ ... OK
* this is package ‘wompwomp’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘wompwomp’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [9s/9s] 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [57s/57s]
[57s/57s] 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 ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('wompwomp_0.99.8.tar.gz')
===============================
── Installing wompwomp ─────────────────────────────────────────────────────────
✔ Package installed successfully
── wompwomp session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvY9BxT/file53e0a47e3ca0d/wompwomp
→ BiocVersion: 3.22
→ Package: wompwomp
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/a59395ce07729b7c2a994d71277d78249fb863b9/wompwomp.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmpvY9BxT/file53e0a47e3ca0d/wompwomp
→ installDir: /tmp/RtmpvY9BxT/file53e0a5150917
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on wompwomp ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* 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...
* 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...
i NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
i and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
• examples-with-labeling.Rmd
• ...
• wompwomp_intro.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of wompwomp...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/plot_alluvial.R (line 165, column 22)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• plot_alluvial.R (line 67, column 15)
• ...
• plot_alluvial.R (line 1524, column 19)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/run_cli.R (line 15, column 9)
• ...
• print() in R/run_plot_alluvial_internal_cli.R (line 151, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/plot_alluvial.R (line 899, column 30)
• R/plot_alluvial.R (line 989, column 38)
* 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 16
functions greater than 50 lines.
The longest 5 functions are:
• determine_crossing_edges() (R/objective_calculation.R): 381 lines
• ...
• data_sort() (R/plot_alluvial.R): 154 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: More than one NEWS file found.See ?news for recognition ordering.
Please remove one of the following:
• inst/NEWS
• wompwomp/NEWS.md
* 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; 882 lines (19%) are > 80 characters long.
First few lines:
• R/cli_utils.R#L5 if (length(i) == 0 || i[1] == length ...
• ...
• vignettes/wompwomp_intro.Rmd#L168 objective_unsorted <- determine_weighted
...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
• R/run_data_sort_cli.R#L23 --matrix_initialization_value_column_or ...
• R/run_data_sort_cli.R#L24 --weight_scalar_column_order Positive i ...
i NOTE: Consider multiples of 4 spaces for line indents; 267 lines (6%) are
not.
First few lines:
• R/objective_calculation.R#L40 public = list( ...
• ...
• R/run_plot_alluvial_internal_cli.R#L62 -q, --quiet Don't show s ...
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 | ⚠ 1 WARNINGS | i 12 NOTES
i See the wompwomp.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.