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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceImpactR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceImpactR_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/SpliceImpactR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-22 02:44:59 UTC
* using option ‘--no-vignettes’
* checking for file ‘SpliceImpactR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpliceImpactR’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.23/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.23/data/annotation/src/contrib/PACKAGES'
 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  8.0Mb
  sub-directories of 1Mb or more:
    extdata   6.7Mb
* 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 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         5.492  0.306   5.543
plot_ppi_summary         5.383  0.344   5.451
integrated_event_summary 5.110  0.059   5.164
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceImpactR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘SpliceImpactR’ ...
** this is package ‘SpliceImpactR’ version ‘1.1.0’
** 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 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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 
 27.856   2.233  26.253