===============================
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_0.99.4.tar.gz’
===============================
BiocCheckGitClone('wompwomp')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11/wompwomp
→ BiocVersion: 3.22
→ Package: wompwomp
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11/wompwomp.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11/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 v1.45.18 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/3936/8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11/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 ‘0.99.4’
* 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 ... NOTE
License stub is invalid DCF.
* 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 ... [10s/10s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) data_sort.Rd:52: Lost braces; missing escapes or markup?
52 | \item{sorting_algorithm}{Character. Algorithm with which to sort the values in the dataframe. Can choose from {'neighbornet', 'tsp', 'greedy_wolf', 'greedy_wblf', 'none'}. 'neighbornet' performs sorting with NeighborNet (Bryant and Moulton, 2004). 'tsp' performs Traveling Salesman Problem solver from the TSP package. greedy_wolf' implements a custom greedy algorithm where one layer is fixed, and the other layer is sorted such that each node is positioned as close to its largest parent from the fixed side as possible in a greedy fashion. 'greedy_wblf' implements the 'greedy_wolf' algorithm described previously twice, treating each column as fixed in one iteration and free in the other iteration. 'greedy_wolf' and 'greedy_wblf' are only valid when \code{graphing_columns} has exactly two entries. 'random' randomly maps blocks. 'none' keeps the mappings as-is when passed into the function.}
| ^
checkRd: (-1) plot_alluvial.Rd:82: Lost braces; missing escapes or markup?
82 | \item{sorting_algorithm}{Character. Algorithm with which to sort the values in the dataframe. Can choose from {'neighbornet', 'tsp', 'greedy_wolf', 'greedy_wblf', 'random', 'none'}. 'neighbornet' performs sorting with NeighborNet (Bryant and Moulton, 2004). 'tsp' performs Traveling Salesman Problem solver from the TSP package. 'greedy_wolf' implements a custom greedy algorithm where one layer is fixed, and the other layer is sorted such that each node is positioned as close to its largest parent from the fixed side as possible in a greedy fashion. 'greedy_wblf' implements the 'greedy_wolf' algorithm described previously twice, treating each column as fixed in one iteration and free in the other iteration. 'greedy_wolf' and 'greedy_wblf' are only valid when \code{graphing_columns} has exactly two entries. 'random' randomly maps blocks. 'none' keeps the mappings as-is when passed into the function.}
| ^
* 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 ... [10s/10s] OK
* 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3936/8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11/wompwomp.Rcheck/00check.log’
for details.
===============================
BiocCheck('wompwomp_0.99.4.tar.gz')
===============================
── Installing wompwomp ─────────────────────────────────────────────────────────
✔ Package installed successfully
── wompwomp session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpe0wwgY/file2ffecb6b5e5bc8/wompwomp
→ BiocVersion: 3.22
→ Package: wompwomp
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3936/8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11/wompwomp.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/Rtmpe0wwgY/file2ffecb6b5e5bc8/wompwomp
→ installDir: /tmp/Rtmpe0wwgY/file2ffecb680ce5ca
→ 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...
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...
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* 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:
• objective_calculation.R (line 393, column 15)
• ...
• plot_alluvial.R (line 1535, 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 157, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/plot_alluvial.R (line 903, column 30)
• R/plot_alluvial.R (line 993, 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 17
functions greater than 50 lines.
The longest 5 functions are:
• determine_crossing_edges() (R/objective_calculation.R): 381 lines
• ...
• run_plot_alluvial_internal_cli() (R/run_plot_alluvial_internal_cli.R): 159
lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• setup_python_env.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
Found in files:
• setup_python_env.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• setup_python_env.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; 902 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#L181 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; 211 lines (4%) are
not.
First few lines:
• R/plot_alluvial.R#L728 group1_na ...
• ...
• R/run_plot_alluvial_internal_cli.R#L64 -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...
✖ 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 v1.45.18 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 16 NOTES
i See the wompwomp.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.