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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1954/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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: 2025-08-30 03:01:37 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 03:11:38 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 601.6 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 (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 ‘1.29.1’
* 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
ssvFeatureBinaryHeatmap 6.432  0.224   6.657
ssvFetchBam             6.154  0.024   6.136
* 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 (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 0 | SKIP 0 | PASS 1291 ]
> 
> proc.time()
   user  system elapsed 
254.446   1.438 250.992 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation2.8850.0942.941
append_ynorm0.0770.0020.047
applyMovingAverage0.6920.0030.684
applySpline0.3880.0020.331
assemble_heatmap_cluster_bars0.7630.0010.731
calc_norm_factors0.0340.0000.023
centerAtMax0.3070.0210.284
centerFixedSizeGRanges0.1960.0100.206
centerGRangesAtMax0.5510.0070.473
clusteringKmeans0.0370.0000.025
clusteringKmeansNestedHclust0.0560.0010.031
col2hex0.0010.0000.001
collapse_gr0.6880.0030.690
convert_collapsed_coord0.1690.0050.174
copy_clust_info1.7550.0031.586
crossCorrByRle0.3970.0050.403
easyLoad_FUN0.0470.0020.049
easyLoad_IDRmerged0.0410.0010.041
easyLoad_bed0.1230.0000.122
easyLoad_broadPeak0.0360.0010.037
easyLoad_narrowPeak0.0340.0010.035
easyLoad_seacr0.0410.0000.040
expandCigar0.1760.0020.145
findMaxPos0.0670.0010.052
fragLen_calcStranded1.5620.0021.546
fragLen_fromMacs2Xls0.0030.0010.002
getReadLength0.0510.0010.052
get_mapped_reads0.0090.0000.008
ggellipse0.5400.0010.542
harmonize_seqlengths0.1150.0000.115
make_clustering_matrix0.0820.0010.070
merge_clusters4.3270.0394.184
prepare_fetch_GRanges0.0280.0000.028
prepare_fetch_GRanges_names0.0770.0000.078
prepare_fetch_GRanges_width0.0270.0000.027
quantileGRangesWidth0.0020.0000.002
reorder_clusters_hclust1.9020.0021.813
reorder_clusters_manual1.0400.0020.959
reorder_clusters_stepdown1.8390.0001.792
reverse_clusters2.0920.0031.968
safeBrew0.0210.0020.023
split_cluster1.8170.0051.722
ssvAnnotateSubjectGRanges1.0180.0031.022
ssvConsensusIntervalSets0.3090.0020.311
ssvFactorizeMembTable0.0100.0020.012
ssvFeatureBars0.5370.0010.537
ssvFeatureBinaryHeatmap6.4320.2246.657
ssvFeatureEuler0.5150.0000.515
ssvFeaturePie0.4750.0030.477
ssvFeatureUpset2.4180.0012.419
ssvFeatureVenn0.8990.0000.899
ssvFetchBam6.1540.0246.136
ssvFetchBamPE1.9340.0091.944
ssvFetchBamPE.RNA1.5610.0201.479
ssvFetchBigwig1.4230.0131.430
ssvFetchGRanges0.7320.0000.732
ssvFetchSignal1.4370.0051.443
ssvMakeMembTable-methods0.5150.0040.519
ssvOverlapIntervalSets0.2290.0000.229
ssvSignalBandedQuantiles3.6430.0663.560
ssvSignalClustering2.6940.0042.556
ssvSignalHeatmap.ClusterBars3.4470.0593.175
ssvSignalHeatmap4.1310.0193.734
ssvSignalLineplot2.2160.0092.211
ssvSignalLineplotAgg0.7980.0030.758
ssvSignalScatterplot0.9320.0040.889
viewGRangesWinSample_dt1.2570.0041.255
viewGRangesWinSummary_dt1.2040.0141.193
within_clust_sort1.6170.1201.674