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R CMD BUILD
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* checking for file ‘scCulturePredict/DESCRIPTION’ ... OK
* preparing ‘scCulturePredict’:
* 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
WARNING: directory ‘scCulturePredict/figure’ is empty
WARNING: directory ‘scCulturePredict/man/figures’ is empty
WARNING: directory ‘scCulturePredict/vignettes/results’ is empty
Omitted ‘LazyData’ from DESCRIPTION
* building ‘scCulturePredict_0.99.32.tar.gz’
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BiocCheckGitClone('scCulturePredict')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3909/scCulturePredict_20250915072657/scCulturePredict
→ BiocVersion: 3.22
→ Package: scCulturePredict
→ PackageVersion: 0.99.32
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3909/scCulturePredict_20250915072657/scCulturePredict.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3909/scCulturePredict_20250915072657/scCulturePredict
→ 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...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3909/scCulturePredict_20250915072657/scCulturePredict.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 ‘scCulturePredict/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scCulturePredict’ version ‘0.99.32’
* 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 ‘scCulturePredict’ 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Matrix’ ‘S4Vectors’ ‘caret’ ‘reshape2’ ‘tools’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [24s/24s] NOTE
create_build_plots: no visible binding for global variable ‘UMAP_1’
create_build_plots: no visible binding for global variable ‘UMAP_2’
create_build_plots: no visible binding for global variable ‘Correct’
create_confidence_plot: no visible binding for global variable ‘UMAP_1’
create_confidence_plot: no visible binding for global variable ‘UMAP_2’
create_confidence_plot: no visible binding for global variable
‘Confidence’
create_evaluation_plots: no visible binding for global variable
‘UMAP_1’
create_evaluation_plots: no visible binding for global variable
‘UMAP_2’
create_predictions_plot: no visible binding for global variable
‘UMAP_1’
create_predictions_plot: no visible binding for global variable
‘UMAP_2’
create_predictions_plot: no visible binding for global variable
‘Predicted_Culture’
predict_by_svm: no visible global function definition for ‘setNames’
process_metadata: no visible global function definition for
‘AddMetaData’
Undefined global functions or variables:
AddMetaData Confidence Correct Predicted_Culture UMAP_1 UMAP_2
setNames
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 ... [28s/28s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [430s/430s]
[430s/430s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3909/scCulturePredict_20250915072657/scCulturePredict.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('scCulturePredict_0.99.32.tar.gz')
===============================
── Installing scCulturePredict ─────────────────────────────────────────────────
✔ Package installed successfully
── scCulturePredict session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/Rtmpv18tp6/file3db35d7fb14474/scCulturePredict
→ BiocVersion: 3.22
→ Package: scCulturePredict
→ PackageVersion: 0.99.32
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3909/scCulturePredict_20250915072657/scCulturePredict.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/Rtmpv18tp6/file3db35d7fb14474/scCulturePredict
→ installDir: /tmp/Rtmpv18tp6/file3db35d71c0d3a6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scCulturePredict ───────────────────────────────────────
* 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 4.3.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (19%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scCulturePredict...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• prediction.R (line 320, column 21)
• preprocessing.R (line 201, column 77)
• preprocessing.R (line 211, column 79)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/data_loading.R (line 195, column 20)
• ...
• R/preprocessing.R (line 148, column 20)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/reduce_dimensions.Rd
i Found @ in vignettes/scCulturePredict-introduction.Rmd
i Found @ in vignettes/scCulturePredict-visualization.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
• load_sce_data() (R/data_loading.R): 289 lines
• ...
• predict_by_svm() (R/prediction.R): 114 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• plot_scCulture.Rd
• scCulture.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• plot_scCulture.Rd
• scCulture.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• plot_scCulture.Rd
• scCulture.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; 276 lines (7%) are > 80 characters long.
First few lines:
• R/data_loading.R#L4 #' Checks for malformed input files (e.g ...
• ...
• vignettes/scCulturePredict-visualization.Rmd#L391 5. **Export Quality**: Save
at appropria ...
i NOTE: Consider multiples of 4 spaces for line indents; 1195 lines (30%) are
not.
First few lines:
• R/data_loading.R#L14 # Input validation ...
• ...
• vignettes/scCulturePredict-visualization.Rmd#L372 theme_publication() ...
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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the scCulturePredict.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.