Zachary Wakefield
| Snapshot Date: 2026-05-01 13:45 -0400 (Fri, 01 May 2026) |
| git_url: https://git.bioconductor.org/packages/SpliceImpactR |
| git_branch: devel |
| git_last_commit: 64b59ab |
| git_last_commit_date: 2026-04-28 09:06:51 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-02 11:33 -0400 (Sat, 02 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4844 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2107/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceImpactR 1.1.0 (landing page) Zachary Wakefield
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for SpliceImpactR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the SpliceImpactR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceImpactR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SpliceImpactR |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:SpliceImpactR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings SpliceImpactR_1.1.0.tar.gz |
| StartedAt: 2026-05-02 04:56:33 -0400 (Sat, 02 May 2026) |
| EndedAt: 2026-05-02 05:07:22 -0400 (Sat, 02 May 2026) |
| EllapsedTime: 649.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceImpactR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:SpliceImpactR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings SpliceImpactR_1.1.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-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: 2026-05-02 08:56:33 UTC
* 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 ... 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 8.1Mb
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 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 17.673 1.892 18.185
plot_ppi_summary 15.650 1.829 15.988
integrated_event_summary 16.543 0.378 16.694
enrich_by_db 11.472 1.023 11.183
get_splicing_impact 8.881 0.140 6.765
enrich_domains_hypergeo 7.555 1.426 7.484
plot_enriched_domains_counts 7.651 0.883 7.157
enrich_by_event 7.417 1.061 7.087
plot_length_comparison 7.213 0.796 7.788
compare_sequence_frame 7.025 0.251 7.123
get_domains 6.262 0.397 6.387
plot_alignment_summary 6.240 0.029 6.110
compare_sequences_alignment 5.739 0.272 5.880
* 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
SpliceImpactR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL SpliceImpactR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-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)
SpliceImpactR.Rcheck/tests/testthat.Rout
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
103.424 11.353 97.028
SpliceImpactR.Rcheck/SpliceImpactR-Ex.timings
| name | user | system | elapsed | |
| add_splice_part | 1.094 | 0.019 | 1.113 | |
| as_dt_from_s4 | 0.100 | 0.008 | 0.107 | |
| as_splice_impact_result | 0.289 | 0.068 | 0.357 | |
| attach_sequences | 1.679 | 0.146 | 1.770 | |
| compare_hit_index | 2.129 | 0.072 | 2.160 | |
| compare_sequence_frame | 7.025 | 0.251 | 7.123 | |
| compare_sequences_alignment | 5.739 | 0.272 | 5.880 | |
| compare_transcript_pairs | 0.087 | 0.004 | 0.070 | |
| enrich_by_db | 11.472 | 1.023 | 11.183 | |
| enrich_by_event | 7.417 | 1.061 | 7.087 | |
| enrich_domains_hypergeo | 7.555 | 1.426 | 7.484 | |
| filter_spliceimpact_hits | 0.538 | 0.069 | 0.607 | |
| get_annotation | 0.043 | 0.005 | 0.048 | |
| get_background | 1.324 | 0.803 | 0.919 | |
| get_comprehensive_annotations | 0.083 | 0.007 | 0.070 | |
| get_di_gene_enrichment | 0 | 0 | 0 | |
| get_differential_inclusion | 1.314 | 0.213 | 1.502 | |
| get_domain_gene_for_enrichment | 0 | 0 | 0 | |
| get_domains | 6.262 | 0.397 | 6.387 | |
| get_enrichment | 0 | 0 | 0 | |
| get_exon_features | 0.155 | 0.000 | 0.127 | |
| get_gene_enrichment | 0.455 | 0.013 | 0.467 | |
| get_hitindex | 0.110 | 0.004 | 0.107 | |
| get_hits_core | 0.003 | 0.000 | 0.002 | |
| get_hits_domain | 0.003 | 0.000 | 0.002 | |
| get_hits_final_view | 0.004 | 0.000 | 0.004 | |
| get_hits_ppi | 0.003 | 0.000 | 0.003 | |
| get_hits_sequence | 0.003 | 0.000 | 0.002 | |
| get_manual_features | 0.066 | 0.000 | 0.055 | |
| get_matched_events_chunked | 1.487 | 0.026 | 1.453 | |
| get_pairs | 1.542 | 0.065 | 1.545 | |
| get_ppi_gene_enrichment | 0 | 0 | 0 | |
| get_ppi_interactions | 1.101 | 0.048 | 1.150 | |
| get_ppi_switches | 17.673 | 1.892 | 18.185 | |
| get_protein_features | 0.034 | 0.002 | 0.036 | |
| get_proximal_shift_from_hits | 2.017 | 0.106 | 2.056 | |
| get_rmats | 0.267 | 0.006 | 0.233 | |
| get_rmats_hit | 0.378 | 0.008 | 0.337 | |
| get_rmats_post_di | 0.021 | 0.000 | 0.022 | |
| get_splicing_impact | 8.881 | 0.140 | 6.765 | |
| get_user_data | 0.012 | 0.000 | 0.009 | |
| get_user_data_post_di | 0.014 | 0.000 | 0.012 | |
| import_di_table | 0.010 | 0.000 | 0.009 | |
| integrated_event_summary | 16.543 | 0.378 | 16.694 | |
| keep_sig_pairs | 1.278 | 0.002 | 1.267 | |
| load_example_data | 0.172 | 0.002 | 0.151 | |
| load_gtf_long | 0.000 | 0.000 | 0.001 | |
| load_rmats | 0.166 | 0.005 | 0.163 | |
| overview_spicing_comparison | 1.189 | 0.004 | 1.136 | |
| plot_alignment_summary | 6.240 | 0.029 | 6.110 | |
| plot_di_volcano_dt | 1.464 | 0.006 | 1.450 | |
| plot_enriched_domains_counts | 7.651 | 0.883 | 7.157 | |
| plot_length_comparison | 7.213 | 0.796 | 7.788 | |
| plot_ppi_summary | 15.650 | 1.829 | 15.988 | |
| plot_two_transcripts_with_domains_unified | 0 | 0 | 0 | |
| probe_individual_event | 1.706 | 0.103 | 1.793 | |
| spliceimpact_s4_guide | 0.000 | 0.000 | 0.001 | |
| spliceimpact_s4_schema | 0 | 0 | 0 | |