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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 1969/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.28.0  (landing page)
Joseph R Boyd
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_21
git_last_commit: 28d6e95
git_last_commit_date: 2025-04-15 11:20:09 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for seqsetvis on nebbiolo1

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: 1.28.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings seqsetvis_1.28.0.tar.gz
StartedAt: 2025-10-16 03:33:36 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 03:44:09 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 632.9 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings seqsetvis_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.28.0’
* 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 ‘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
ssvFeatureBinaryHeatmap 7.277  0.169   7.447
ssvFetchBam             5.844  0.007   5.817
ssvSignalHeatmap        5.780  0.062   5.467
* 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-3.21-bioc/R/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘seqsetvis’ ...
** this is package ‘seqsetvis’ version ‘1.28.0’
** 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 (2025-06-13) -- "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 
265.479   1.652 261.536 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.2810.1013.346
append_ynorm0.0750.0010.045
applyMovingAverage0.9090.0000.899
applySpline0.4720.0020.437
assemble_heatmap_cluster_bars0.9330.0270.926
calc_norm_factors0.0350.0000.024
centerAtMax0.3460.0080.262
centerFixedSizeGRanges0.1230.0050.129
centerGRangesAtMax0.5950.0050.493
clusteringKmeans0.0370.0030.026
clusteringKmeansNestedHclust0.0550.0020.031
col2hex0.0010.0000.001
collapse_gr0.6450.0040.649
convert_collapsed_coord0.1630.0040.167
copy_clust_info1.8480.0151.700
crossCorrByRle0.3380.0040.343
easyLoad_FUN0.0470.0000.048
easyLoad_IDRmerged0.0380.0010.040
easyLoad_bed0.1140.0000.114
easyLoad_broadPeak0.0320.0000.033
easyLoad_narrowPeak0.0490.0010.050
easyLoad_seacr0.0380.0000.039
expandCigar0.1770.0010.146
findMaxPos0.0480.0050.037
fragLen_calcStranded1.6300.0011.619
fragLen_fromMacs2Xls0.0030.0000.002
getReadLength0.0460.0010.048
get_mapped_reads0.0080.0000.008
ggellipse0.8530.0020.855
harmonize_seqlengths0.1060.0040.111
make_clustering_matrix0.0770.0020.066
merge_clusters4.2730.0264.208
prepare_fetch_GRanges0.0320.0010.033
prepare_fetch_GRanges_names0.0830.0020.084
prepare_fetch_GRanges_width0.0440.0090.052
quantileGRangesWidth0.0030.0010.003
reorder_clusters_hclust2.3320.0022.285
reorder_clusters_manual1.2950.0151.231
reorder_clusters_stepdown3.2450.0993.300
reverse_clusters2.4390.0142.341
safeBrew0.0210.0010.021
split_cluster2.2260.0442.109
ssvAnnotateSubjectGRanges0.9180.0160.934
ssvConsensusIntervalSets0.3170.0000.318
ssvFactorizeMembTable0.0120.0030.015
ssvFeatureBars0.8590.0010.861
ssvFeatureBinaryHeatmap7.2770.1697.447
ssvFeatureEuler0.7790.0070.785
ssvFeaturePie0.6120.0020.614
ssvFeatureUpset3.1680.0033.172
ssvFeatureVenn1.3850.0031.389
ssvFetchBam5.8440.0075.817
ssvFetchBamPE1.8840.0051.896
ssvFetchBamPE.RNA1.5150.0031.427
ssvFetchBigwig1.2810.0021.278
ssvFetchGRanges0.7170.0020.718
ssvFetchSignal1.4730.0071.479
ssvMakeMembTable-methods0.4690.0030.472
ssvOverlapIntervalSets0.2190.0040.223
ssvSignalBandedQuantiles3.9290.0043.783
ssvSignalClustering3.0550.0032.926
ssvSignalHeatmap.ClusterBars4.1600.0033.931
ssvSignalHeatmap5.7800.0625.467
ssvSignalLineplot2.7490.0032.747
ssvSignalLineplotAgg0.9620.0030.946
ssvSignalScatterplot1.1420.0021.100
viewGRangesWinSample_dt1.1180.0031.116
viewGRangesWinSummary_dt1.1160.0031.070
within_clust_sort1.7090.0021.652