Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-10-16 12:04 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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: 2025-10-15 13:45 -0400 (Wed, 15 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 12.7.6 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings seqsetvis_1.29.1.tar.gz
StartedAt: 2025-10-16 04:54:04 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 05:07:34 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 809.9 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings seqsetvis_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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 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
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
ssvFetchBamPE.RNA            16.938  0.069   2.844
ssvSignalHeatmap             12.816  0.302   6.637
ssvSignalHeatmap.ClusterBars 11.342  0.354   6.344
ssvSignalClustering           9.696  0.211   5.389
ssvSignalBandedQuantiles      7.929  0.028   4.986
merge_clusters                7.509  0.284   5.533
ssvFeatureBinaryHeatmap       7.044  0.496   7.653
ssvFetchBam                   7.369  0.089   7.425
split_cluster                 5.737  0.208   3.390
add_cluster_annotation        5.716  0.191   4.945
applySpline                   5.704  0.038   1.031
reorder_clusters_stepdown     4.889  0.390   4.383
* 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


Installation output

seqsetvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> 
> ## 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 
412.995   5.331 336.297 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation5.7160.1914.945
append_ynorm0.1280.0000.055
applyMovingAverage1.9410.0061.215
applySpline5.7040.0381.031
assemble_heatmap_cluster_bars2.5060.0201.560
calc_norm_factors0.2590.0010.098
centerAtMax1.8910.0120.511
centerFixedSizeGRanges0.2220.0040.226
centerGRangesAtMax2.6650.0570.922
clusteringKmeans0.1390.0020.052
clusteringKmeansNestedHclust0.1000.0040.057
col2hex0.0020.0000.002
collapse_gr0.9150.0220.938
convert_collapsed_coord0.3740.0060.379
copy_clust_info3.7270.1562.779
crossCorrByRle0.5680.0110.671
easyLoad_FUN0.0720.0000.080
easyLoad_IDRmerged0.0630.0010.077
easyLoad_bed0.2080.0000.208
easyLoad_broadPeak0.0560.0000.060
easyLoad_narrowPeak0.0460.0000.056
easyLoad_seacr0.0440.0000.044
expandCigar0.1860.0010.169
findMaxPos0.0710.0010.039
fragLen_calcStranded2.7400.0071.963
fragLen_fromMacs2Xls0.0030.0000.002
getReadLength0.0520.0000.052
get_mapped_reads0.0090.0000.009
ggellipse0.9980.0021.017
harmonize_seqlengths0.1340.0060.139
make_clustering_matrix0.3000.0010.140
merge_clusters7.5090.2845.533
prepare_fetch_GRanges0.0280.0050.033
prepare_fetch_GRanges_names0.0780.0050.083
prepare_fetch_GRanges_width0.0270.0020.029
quantileGRangesWidth0.0020.0000.002
reorder_clusters_hclust3.8600.1513.090
reorder_clusters_manual3.0680.1321.851
reorder_clusters_stepdown4.8890.3904.383
reverse_clusters3.9650.2183.129
safeBrew0.0260.0020.028
split_cluster5.7370.2083.390
ssvAnnotateSubjectGRanges1.1720.0421.226
ssvConsensusIntervalSets0.3440.0030.355
ssvFactorizeMembTable0.0140.0010.015
ssvFeatureBars1.0010.0181.022
ssvFeatureBinaryHeatmap7.0440.4967.653
ssvFeatureEuler1.0140.0471.076
ssvFeaturePie0.8160.0240.840
ssvFeatureUpset4.1190.0694.280
ssvFeatureVenn1.8850.0281.914
ssvFetchBam7.3690.0897.425
ssvFetchBamPE2.5260.0492.663
ssvFetchBamPE.RNA16.938 0.069 2.844
ssvFetchBigwig2.1800.0062.202
ssvFetchGRanges1.2040.0011.207
ssvFetchSignal2.1740.0052.180
ssvMakeMembTable-methods0.8330.0010.833
ssvOverlapIntervalSets0.3460.0010.347
ssvSignalBandedQuantiles7.9290.0284.986
ssvSignalClustering9.6960.2115.389
ssvSignalHeatmap.ClusterBars11.342 0.354 6.344
ssvSignalHeatmap12.816 0.302 6.637
ssvSignalLineplot3.9770.1474.139
ssvSignalLineplotAgg1.2140.0151.157
ssvSignalScatterplot1.3510.0181.325
viewGRangesWinSample_dt1.3910.0151.427
viewGRangesWinSummary_dt2.6930.0551.775
within_clust_sort3.9730.2403.064