===============================
BiocCheckGitClone('SpliceImpactR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/25ae9d13179e33be609b6479fb62d4c7432328eb/SpliceImpactR
→ BiocVersion: 3.23
→ Package: SpliceImpactR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/25ae9d13179e33be609b6479fb62d4c7432328eb/SpliceImpactR.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/25ae9d13179e33be609b6479fb62d4c7432328eb/SpliceImpactR
→ 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 v1.47.20 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/3772/25ae9d13179e33be609b6479fb62d4c7432328eb/SpliceImpactR.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-23 18:02:54 UTC
* using option ‘--no-vignettes’
* checking for file ‘SpliceImpactR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpliceImpactR’ 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 ‘SpliceImpactR’ can be installed ... OK
* checking installed package size ... INFO
installed size is 6.3Mb
sub-directories of 1Mb or more:
extdata 4.9Mb
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [42s/42s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'compare_hit_index.Rd':
\examples lines wider than 100 characters:
hit_compare <- compare_hit_index(sample_frame, condition_map = c(control = "control", test = "case"))
Rd file 'enrich_by_db.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'enrich_by_event.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'enrich_domains_hypergeo.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'get_background.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annots$annotations, timeout = 600, test = TRUE)
Rd file 'get_comprehensive_annotations.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'get_di_gene_enrichment.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
enrichment <- get_enrichment(get_di_gene_enrichment(res, .05, .1), bg$gene_id, species = 'human', 'ensembl', 'MSigDB:H')
Rd file 'get_domain_gene_for_enrichment.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
enrichment <- get_enrichment(get_domain_gene_for_enrichment(hits_domain), bg$gene_id, species = 'human', 'ensembl', 'MSigDB:H')
Rd file 'get_domains.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'get_enrichment.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'get_exon_features.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'get_ppi_gene_enrichment.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
enrichment <- get_enrichment(get_ppi_gene_enrichment(hits_final), bg$gene_id, species = 'human', 'ensembl', 'MSigDB:H')
Rd file 'get_ppi_switches.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'get_protein_features.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, annotation_df$sequences, timeout = 600, test = TRUE ... [TRUNCATED]
Rd file 'get_rmats.Rd':
\examples lines wider than 100 characters:
rmats <- get_rmats(load_rmats(sample_frame, use = "JCEC", event_types = c("MXE", "SE", "A3SS", "A5SS", "RI")))
Rd file 'get_rmats_hit.Rd':
\examples lines wider than 100 characters:
data <- get_rmats_hit(sample_frame, event_types = c("ALE", "AFE", "MXE", "SE", "A3SS", "A5SS", "RI"))
Rd file 'integrated_event_summary.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'plot_enriched_domains_counts.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
Rd file 'plot_ppi_summary.Rd':
\examples lines wider than 100 characters:
interpro_features <- get_protein_features(c("interpro"), annotation_df$annotations, timeout = 600, test = TRUE)
These lines will be truncated in the PDF manual.
* 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 ... [187s/177s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_ppi_switches 15.221 1.068 15.418
plot_ppi_summary 14.822 0.843 14.799
integrated_event_summary 15.218 0.312 15.236
enrich_by_db 9.200 0.616 8.961
get_splicing_impact 7.949 0.209 6.018
plot_enriched_domains_counts 6.963 0.552 6.647
enrich_domains_hypergeo 6.678 0.558 6.354
enrich_by_event 6.663 0.562 6.351
plot_alignment_summary 6.527 0.077 6.403
compare_sequence_frame 6.107 0.286 6.203
plot_length_comparison 5.706 0.092 5.595
get_domains 5.597 0.098 5.458
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [90s/81s]
[91s/82s] 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 ... [6s/6s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3772/25ae9d13179e33be609b6479fb62d4c7432328eb/SpliceImpactR.Rcheck/00check.log’
for details.
===============================
BiocCheck('SpliceImpactR_0.99.4.tar.gz')
===============================
── Installing SpliceImpactR ────────────────────────────────────────────────────
✔ Package installed successfully
── SpliceImpactR session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpy0rYRN/file170fa466857954/SpliceImpactR
→ BiocVersion: 3.23
→ Package: SpliceImpactR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/25ae9d13179e33be609b6479fb62d4c7432328eb/SpliceImpactR.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/Rtmpy0rYRN/file170fa466857954/SpliceImpactR
→ installDir: /tmp/Rtmpy0rYRN/file170fa427bc7a67
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpliceImpactR ──────────────────────────────────────────
* 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 3.5.0 to 4.6.0
* 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...
i NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (43%).
* 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:
• SpliceImpactR.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SpliceImpactR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/compare_seqs.R (line 292, column 24)
• ...
• cat() in R/summarized_experiment_utils.R (line 587, column 3)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/get_annotations.R (line 1193, column 10)
• R/get_protein_feature_visualizations.R (line 257, column 24)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/get_protein_feature_visualizations.R (line 187, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 47 times)
• suppressWarnings() in R/get_annotations.R (line 410, column 64)
• ...
• suppressWarnings() in R/summarized_experiment_utils.R (line 76, column 8)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 56
functions greater than 50 lines.
The longest 5 functions are:
• get_enrichment() (R/get_multi_analysis.R): 388 lines
• ...
• get_protein_features() (R/get_protein_features.R): 228 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• get_di_gene_enrichment.Rd
• ...
• plot_two_transcripts_with_domains_unified.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
Found in files:
• get_di_gene_enrichment.Rd
• ...
• plot_two_transcripts_with_domains_unified.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; 901 lines (6%) are > 80 characters long.
First few lines:
• R/compare_seqs.R#L108 #' @param annotations Annotation data.ta ...
• ...
• vignettes/SpliceImpactR.Rmd#L743 - `get_hits_domain()`: domain gain/loss ...
i NOTE: Consider multiples of 4 spaces for line indents; 5024 lines (34%) are
not.
First few lines:
• R/compare_seqs.R#L15 ap <- as.character(pwalign::alignedPat ...
• ...
• vignettes/SpliceImpactR.Rmd#L990 annotations = annotation_df$annotation ...
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 v1.47.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 13 NOTES
i See the SpliceImpactR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.