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This page was generated on 2025-10-09 12:04 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1969/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 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 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: 2025-10-09 04:42:46 -0400 (Thu, 09 Oct 2025)
EndedAt: 2025-10-09 04:55:06 -0400 (Thu, 09 Oct 2025)
EllapsedTime: 739.8 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            13.825  0.096   2.302
ssvSignalHeatmap             12.148  0.199   6.428
ssvFeatureBinaryHeatmap       9.482  0.664  10.147
ssvSignalHeatmap.ClusterBars  9.511  0.029   5.142
ssvSignalClustering           8.873  0.029   4.120
merge_clusters                8.281  0.201   6.648
ssvFetchBam                   7.455  0.077   7.506
ssvSignalBandedQuantiles      7.200  0.032   4.533
split_cluster                 5.616  0.046   3.070
add_cluster_annotation        5.486  0.128   4.742
applySpline                   5.556  0.021   0.802
* 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 
359.080   3.099 287.787 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation5.4860.1284.742
append_ynorm0.1290.0040.055
applyMovingAverage2.0200.0061.234
applySpline5.5560.0210.802
assemble_heatmap_cluster_bars2.6800.0211.797
calc_norm_factors0.1010.0010.046
centerAtMax1.9500.0070.599
centerFixedSizeGRanges0.2950.0070.302
centerGRangesAtMax2.9390.0421.004
clusteringKmeans0.0930.0020.031
clusteringKmeansNestedHclust0.0770.0020.038
col2hex0.0020.0000.002
collapse_gr0.7370.0050.742
convert_collapsed_coord0.2790.0010.281
copy_clust_info3.5520.0262.622
crossCorrByRle0.7900.0400.832
easyLoad_FUN0.0960.0030.099
easyLoad_IDRmerged0.0800.0070.088
easyLoad_bed0.2180.0090.226
easyLoad_broadPeak0.0600.0040.064
easyLoad_narrowPeak0.0640.0040.069
easyLoad_seacr0.0690.0050.073
expandCigar0.2920.0020.274
findMaxPos0.1730.0030.095
fragLen_calcStranded3.1950.0312.371
fragLen_fromMacs2Xls0.0030.0000.003
getReadLength0.0830.0010.084
get_mapped_reads0.0130.0000.013
ggellipse1.2550.0031.258
harmonize_seqlengths0.1440.0000.144
make_clustering_matrix0.1280.0010.076
merge_clusters8.2810.2016.648
prepare_fetch_GRanges0.0410.0000.042
prepare_fetch_GRanges_names0.1070.0010.108
prepare_fetch_GRanges_width0.0570.0010.058
quantileGRangesWidth0.0020.0010.004
reorder_clusters_hclust4.3420.0053.208
reorder_clusters_manual2.4550.0071.492
reorder_clusters_stepdown3.6590.0072.616
reverse_clusters4.8610.0183.691
safeBrew0.0260.0010.026
split_cluster5.6160.0463.070
ssvAnnotateSubjectGRanges1.1530.0211.182
ssvConsensusIntervalSets0.3580.0070.365
ssvFactorizeMembTable0.0220.0000.022
ssvFeatureBars1.5430.0571.600
ssvFeatureBinaryHeatmap 9.482 0.66410.147
ssvFeatureEuler0.9070.0420.949
ssvFeaturePie0.7380.0130.751
ssvFeatureUpset3.8270.0953.922
ssvFeatureVenn1.4950.0021.498
ssvFetchBam7.4550.0777.506
ssvFetchBamPE2.3190.0662.386
ssvFetchBamPE.RNA13.825 0.096 2.302
ssvFetchBigwig1.3850.0071.393
ssvFetchGRanges1.0300.0031.033
ssvFetchSignal1.8150.0051.820
ssvMakeMembTable-methods0.5210.0030.524
ssvOverlapIntervalSets0.2260.0010.227
ssvSignalBandedQuantiles7.2000.0324.533
ssvSignalClustering8.8730.0294.120
ssvSignalHeatmap.ClusterBars9.5110.0295.142
ssvSignalHeatmap12.148 0.199 6.428
ssvSignalLineplot3.8160.2734.084
ssvSignalLineplotAgg1.7370.0961.774
ssvSignalScatterplot1.4560.0851.487
viewGRangesWinSample_dt1.3800.0591.433
viewGRangesWinSummary_dt2.0340.0191.264
within_clust_sort3.4660.1512.675