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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SpliceImpactR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SpliceImpactR_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SpliceImpactR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 09:33:35 UTC
* checking for file ‘SpliceImpactR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpliceImpactR’ version ‘1.0.0’
* 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 ‘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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
get_ppi_switches             18.403  2.019  18.957
plot_ppi_summary             16.570  1.956  17.188
integrated_event_summary     17.604  0.407  17.713
enrich_by_db                 11.106  1.004  10.763
get_splicing_impact           9.033  0.101   6.967
plot_enriched_domains_counts  7.907  1.092   7.461
enrich_domains_hypergeo       7.428  1.139   7.232
enrich_by_event               7.346  1.052   7.127
compare_sequence_frame        6.907  0.335   7.080
get_domains                   6.438  0.373   6.540
plot_length_comparison        6.412  0.233   6.479
plot_alignment_summary        6.477  0.106   6.398
compare_sequences_alignment   5.807  0.183   5.827
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SpliceImpactR
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SpliceImpactR’ ...
** this is package ‘SpliceImpactR’ version ‘1.0.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpliceImpactR)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SpliceImpactR)
> 
> test_check("SpliceImpactR")
[INFO] Loading bundled test annotation data
[INFO] Filtered 0 unannotated ALE/AFE events (223 -> 223)
Chunk 1/1: rows 1..40
[1] "[INFO] Processing 13 transcript and protein sequence alignments, this may take a little..."
[1] "[Processing] Identifying frame shifts and rescues"
[1] "[INFO] 0 frameshifts (0 rescues) and 8 non-frameshifts were identified, "
[INFO] Loading bundled test annotation data
[INFO] Loading bundled test annotation data
[INFO] Filtered 0 unannotated ALE/AFE events (465 -> 465)
[INFO] Input contains 41 genes, 605 events, and 2932 event instances.
[PROCESSING/INFO] Filtering out low-coverage rows removed 892 event instances; 4971
remain.
[PROCESSING/INFO] Completing AFE/ALE with zeros per sample (total strategy: event_max)
filled 407 AFE rows and 160 ALE rows (totals: AFE=608, ALE=424).
[PROCESSING/INFO] Filtering genes with no nonzero values per sample/event_type removed
37 genes from specific sample groups; 40 genes remain overall.
[PROCESSING/INFO] Filtering by minimum condition presence removed 211 events; 351
events remain.
[PROCESSING/INFO] Removed 62 non-changing events; 289 events remain.
[PROCESSING/INFO] Filtering events not represented in both conditions removed 30
events; 259 events remain.
[PROCESSING] Fitting quasi-binomial GLMs per site...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

[DONE] Fitted 531 sites in 1 chunks.
[INFO] Done.
Chunk 1/1: rows 1..94
[1] "[INFO] Processing 36 transcript and protein sequence alignments, this may take a little..."
[1] "[Processing] Identifying frame shifts and rescues"
[1] "[INFO] 1 frameshifts (0 rescues) and 27 non-frameshifts were identified, "

[INFO] Loading bundled test annotation data
[INFO] Loading bundled test annotation data
[INFO] Loading bundled test annotation data
[INFO] Filtered 0 unannotated ALE/AFE events (465 -> 465)
[INFO] Filtered 0 unannotated ALE/AFE events (465 -> 465)


[INFO] Loading bundled test annotation data
[INFO] Loading bundled test annotation data
[INFO] Filtered 0 unannotated ALE/AFE events (107 -> 107)
[INFO] Loading bundled test annotation data
[INFO] Loading bundled test annotation data
[INFO] Loading bundled test annotation data
[INFO] Filtered 0 unannotated ALE/AFE events (465 -> 465)
Chunk 1/1: rows 1..94
[INFO] Filtered 0 unannotated ALE/AFE events (465 -> 465)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 163 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-keep_sig_pairs.R:2:3',
  'test-overview_spicing_comparison.R:3:3'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 163 ]
> 
> proc.time()
   user  system elapsed 
100.211  12.042  94.247