| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-31 11:33 -0400 (Tue, 31 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4606 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4534 |
| 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 1996/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqsetvis 1.31.2 (landing page) Joseph R Boyd
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| See other builds for seqsetvis in R Universe. | ||||||||||||||
|
To the developers/maintainers of the seqsetvis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqsetvis.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: seqsetvis |
| Version: 1.31.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.31.2.tar.gz |
| StartedAt: 2026-03-30 21:41:26 -0400 (Mon, 30 Mar 2026) |
| EndedAt: 2026-03-30 21:45:08 -0400 (Mon, 30 Mar 2026) |
| EllapsedTime: 221.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqsetvis.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.31.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/seqsetvis.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* 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: 2026-03-31 01:41:27 UTC
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.31.2’
* 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 ‘seqsetvis’ can be installed ... OK
* checking installed package size ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘seqsetvis’ ... ** this is package ‘seqsetvis’ version ‘1.31.2’ ** using staged installation ** R ** data ** 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 (seqsetvis)
seqsetvis.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-03-28 r89739)
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.
>
> ## load dependencies
> library(testthat)
> library(seqsetvis)
Loading required package: ggplot2
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> ## test package
> test_check(package = "seqsetvis")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1291 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1291 ]
>
> proc.time()
user system elapsed
86.632 1.533 89.622
seqsetvis.Rcheck/seqsetvis-Ex.timings
| name | user | system | elapsed | |
| add_cluster_annotation | 1.204 | 0.025 | 1.238 | |
| append_ynorm | 0.028 | 0.003 | 0.032 | |
| applyMovingAverage | 0.319 | 0.007 | 0.343 | |
| applySpline | 0.160 | 0.005 | 0.167 | |
| assemble_heatmap_cluster_bars | 0.295 | 0.005 | 0.303 | |
| calc_norm_factors | 0.011 | 0.001 | 0.012 | |
| centerAtMax | 0.093 | 0.004 | 0.105 | |
| centerFixedSizeGRanges | 0.050 | 0.005 | 0.061 | |
| centerGRangesAtMax | 0.173 | 0.007 | 0.190 | |
| clusteringKmeans | 0.012 | 0.001 | 0.014 | |
| clusteringKmeansNestedHclust | 0.014 | 0.001 | 0.016 | |
| col2hex | 0.001 | 0.001 | 0.001 | |
| collapse_gr | 0.239 | 0.006 | 0.249 | |
| convert_collapsed_coord | 0.063 | 0.004 | 0.068 | |
| copy_clust_info | 0.562 | 0.008 | 0.584 | |
| crossCorrByRle | 0.151 | 0.004 | 0.155 | |
| easyLoad_FUN | 0.016 | 0.000 | 0.018 | |
| easyLoad_IDRmerged | 0.013 | 0.000 | 0.015 | |
| easyLoad_bed | 0.037 | 0.000 | 0.038 | |
| easyLoad_broadPeak | 0.012 | 0.001 | 0.012 | |
| easyLoad_narrowPeak | 0.013 | 0.001 | 0.013 | |
| easyLoad_seacr | 0.013 | 0.001 | 0.013 | |
| expandCigar | 0.051 | 0.002 | 0.053 | |
| findMaxPos | 0.014 | 0.002 | 0.016 | |
| fragLen_calcStranded | 0.480 | 0.003 | 0.484 | |
| fragLen_fromMacs2Xls | 0.001 | 0.001 | 0.002 | |
| getReadLength | 0.016 | 0.001 | 0.017 | |
| get_mapped_reads | 0.003 | 0.000 | 0.003 | |
| ggellipse | 0.269 | 0.003 | 0.272 | |
| harmonize_seqlengths | 0.038 | 0.003 | 0.041 | |
| make_clustering_matrix | 0.027 | 0.002 | 0.028 | |
| merge_clusters | 1.301 | 0.014 | 1.333 | |
| prepare_fetch_GRanges | 0.010 | 0.001 | 0.011 | |
| prepare_fetch_GRanges_names | 0.032 | 0.001 | 0.035 | |
| prepare_fetch_GRanges_width | 0.010 | 0.001 | 0.011 | |
| quantileGRangesWidth | 0.001 | 0.001 | 0.001 | |
| reorder_clusters_hclust | 0.739 | 0.007 | 0.774 | |
| reorder_clusters_manual | 0.425 | 0.008 | 0.437 | |
| reorder_clusters_stepdown | 1.147 | 0.010 | 1.192 | |
| reverse_clusters | 0.841 | 0.017 | 0.872 | |
| safeBrew | 0.009 | 0.001 | 0.010 | |
| split_cluster | 0.682 | 0.011 | 0.709 | |
| ssvAnnotateSubjectGRanges | 0.310 | 0.009 | 0.320 | |
| ssvConsensusIntervalSets | 0.106 | 0.005 | 0.113 | |
| ssvFactorizeMembTable | 0.005 | 0.001 | 0.005 | |
| ssvFeatureBars | 0.262 | 0.003 | 0.266 | |
| ssvFeatureBinaryHeatmap | 2.968 | 0.032 | 3.024 | |
| ssvFeatureEuler | 0.269 | 0.003 | 0.273 | |
| ssvFeaturePie | 0.198 | 0.002 | 0.201 | |
| ssvFeatureUpset | 1.023 | 0.009 | 1.041 | |
| ssvFeatureVenn | 0.465 | 0.004 | 0.471 | |
| ssvFetchBam | 1.812 | 0.025 | 1.850 | |
| ssvFetchBamPE | 0.593 | 0.009 | 0.603 | |
| ssvFetchBamPE.RNA | 0.505 | 0.022 | 0.534 | |
| ssvFetchBigwig | 0.424 | 0.007 | 0.433 | |
| ssvFetchGRanges | 0.247 | 0.005 | 0.256 | |
| ssvFetchSignal | 0.855 | 0.011 | 0.873 | |
| ssvMakeMembTable-methods | 0.161 | 0.006 | 0.168 | |
| ssvOverlapIntervalSets | 0.079 | 0.004 | 0.084 | |
| ssvSignalBandedQuantiles | 1.243 | 0.027 | 1.297 | |
| ssvSignalClustering | 1.110 | 0.035 | 1.182 | |
| ssvSignalHeatmap.ClusterBars | 2.148 | 0.050 | 2.286 | |
| ssvSignalHeatmap | 1.941 | 0.045 | 2.059 | |
| ssvSignalLineplot | 0.992 | 0.013 | 1.021 | |
| ssvSignalLineplotAgg | 0.364 | 0.008 | 0.379 | |
| ssvSignalScatterplot | 0.439 | 0.013 | 0.462 | |
| viewGRangesWinSample_dt | 0.393 | 0.007 | 0.405 | |
| viewGRangesWinSummary_dt | 0.394 | 0.011 | 0.420 | |
| within_clust_sort | 0.630 | 0.013 | 0.653 | |