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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 1974/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: c75429d
git_last_commit_date: 2025-07-23 17:50:06 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for seqsetvis on kjohnson3

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.

raw results


Summary

Package: seqsetvis
Version: 1.29.1
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_1.29.1.tar.gz
StartedAt: 2025-10-10 21:43:22 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 21:46:49 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 207.5 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.29.1’
* 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


Installation output

seqsetvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘seqsetvis’ ...
** this is package ‘seqsetvis’ version ‘1.29.1’
** 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)

Tests output

seqsetvis.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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)
> 
> ## 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 
 80.680   1.776  83.029 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation1.1910.0211.227
append_ynorm0.0230.0030.048
applyMovingAverage0.2950.0040.307
applySpline0.1510.0050.226
assemble_heatmap_cluster_bars0.2850.0040.298
calc_norm_factors0.0100.0010.012
centerAtMax0.0800.0020.082
centerFixedSizeGRanges0.0450.0030.048
centerGRangesAtMax0.1800.0060.186
clusteringKmeans0.0110.0030.014
clusteringKmeansNestedHclust0.0130.0030.016
col2hex0.0000.0000.001
collapse_gr0.2210.0050.229
convert_collapsed_coord0.0730.0040.079
copy_clust_info0.5350.0070.548
crossCorrByRle0.1300.0040.135
easyLoad_FUN0.0150.0000.016
easyLoad_IDRmerged0.0120.0010.013
easyLoad_bed0.0370.0000.037
easyLoad_broadPeak0.0190.0010.019
easyLoad_narrowPeak0.0120.0000.013
easyLoad_seacr0.0120.0010.012
expandCigar0.0460.0040.049
findMaxPos0.0130.0030.016
fragLen_calcStranded0.4870.0080.497
fragLen_fromMacs2Xls0.0010.0000.001
getReadLength0.0170.0010.018
get_mapped_reads0.0030.0000.003
ggellipse0.2650.0050.270
harmonize_seqlengths0.0390.0050.042
make_clustering_matrix0.0270.0020.029
merge_clusters1.2660.0101.301
prepare_fetch_GRanges0.0090.0000.010
prepare_fetch_GRanges_names0.0230.0010.025
prepare_fetch_GRanges_width0.0090.0000.009
quantileGRangesWidth0.0010.0010.002
reorder_clusters_hclust1.0710.0071.083
reorder_clusters_manual0.3740.0050.383
reorder_clusters_stepdown0.6760.0050.681
reverse_clusters0.7740.0090.783
safeBrew0.0090.0010.010
split_cluster0.6650.0080.675
ssvAnnotateSubjectGRanges0.2880.0070.297
ssvConsensusIntervalSets0.0990.0040.107
ssvFactorizeMembTable0.0040.0010.005
ssvFeatureBars0.2600.0020.262
ssvFeatureBinaryHeatmap3.1130.2393.382
ssvFeatureEuler0.2640.0060.272
ssvFeaturePie0.2040.0020.209
ssvFeatureUpset1.0230.0161.046
ssvFeatureVenn0.4700.0040.474
ssvFetchBam1.7940.0381.833
ssvFetchBamPE0.5850.0290.621
ssvFetchBamPE.RNA0.4840.0240.511
ssvFetchBigwig0.4110.0040.419
ssvFetchGRanges0.2270.0010.227
ssvFetchSignal0.4810.0270.514
ssvMakeMembTable-methods0.1680.0030.172
ssvOverlapIntervalSets0.0780.0040.081
ssvSignalBandedQuantiles1.2260.0311.275
ssvSignalClustering0.9750.0211.012
ssvSignalHeatmap.ClusterBars1.3290.0201.390
ssvSignalHeatmap1.8300.0491.906
ssvSignalLineplot0.8590.0060.870
ssvSignalLineplotAgg0.3100.0050.321
ssvSignalScatterplot0.3470.0050.357
viewGRangesWinSample_dt0.3380.0070.348
viewGRangesWinSummary_dt0.3320.0090.349
within_clust_sort0.5420.0130.572