===============================
BiocCheckGitClone('SpliceImpactR')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/97a3b687c5be267f36d9725268294fca238fbd9f/SpliceImpactR
BiocVersion: 3.23
Package: SpliceImpactR
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/97a3b687c5be267f36d9725268294fca238fbd9f/SpliceImpactR.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/97a3b687c5be267f36d9725268294fca238fbd9f/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/3772/97a3b687c5be267f36d9725268294fca238fbd9f/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 17:23:27 UTC
* using option --no-vignettes
* checking for file SpliceImpactR/DESCRIPTION ... OK
* checking extension type ... Package
* this is package SpliceImpactR version 0.99.3
* 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 ... [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 ... [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 ... [43s/43s] 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 ... [73s/68s] ERROR
Running examples in SpliceImpactR-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_gene_enrichment
> ### Title: Unified gene selector for enrichment foregrounds
> ### Aliases: get_gene_enrichment
>
> ### ** Examples
>
> res <- data.table::data.table(
+ gene_id = c("ENSG000001", "ENSG000001", "ENSG000002"),
+ padj = c(0.01, 0.20, 0.03),
+ delta_psi = c(0.25, 0.05, -0.30)
+ )
> hits <- data.table::data.table(
+ gene_id = c("ENSG000001", "ENSG000002", "ENSG000003"),
+ n_ppi = c(1L, 0L, 2L),
+ diff_n = c(0L, 1L, 2L)
+ )
> get_gene_enrichment(mode = "di", res = res)
[1] "ENSG000001" "ENSG000002"
> get_gene_enrichment(mode = "ppi", hits = hits)
[1] "ENSG000001" "ENSG000003"
> get_gene_enrichment(mode = "domain", hits = hits)
[1] "ENSG000002" "ENSG000003"
>
> obj <- as_splice_impact_result(res = res, hits_final = hits)
Error in as_granges_res(res) :
as_granges_res: missing required columns: event_id, form, inc, exc, chr, strand
Calls: as_splice_impact_result ... <Anonymous> -> initialize -> initialize -> as_granges_res
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrich_by_db 9.169 0.618 8.924
enrich_by_event 6.637 0.575 6.329
enrich_domains_hypergeo 6.612 0.567 6.301
compare_sequence_frame 6.113 0.304 6.228
get_domains 5.596 0.103 5.461
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [91s/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 ERROR, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3772/97a3b687c5be267f36d9725268294fca238fbd9f/SpliceImpactR.Rcheck/00check.log
for details.
===============================
BiocCheck('SpliceImpactR_0.99.3.tar.gz')
===============================
Installing SpliceImpactR
Package installed successfully
SpliceImpactR session metadata
sourceDir: /tmp/RtmphF3KCH/file16f6fa682e623e/SpliceImpactR
BiocVersion: 3.23
Package: SpliceImpactR
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3772/97a3b687c5be267f36d9725268294fca238fbd9f/SpliceImpactR.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmphF3KCH/file16f6fa682e623e/SpliceImpactR
installDir: /tmp/RtmphF3KCH/file16f6fa1e2865a9
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.