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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1963/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 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: 2025-09-22 04:14:14 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 04:26:54 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 759.8 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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            16.980  0.025   2.322
ssvSignalHeatmap             13.728  0.414   8.088
ssvSignalHeatmap.ClusterBars 11.285  0.115   6.920
ssvFeatureBinaryHeatmap      10.208  0.848  11.056
ssvFetchBam                  10.692  0.199  10.860
ssvSignalBandedQuantiles      9.567  0.155   6.649
ssvSignalClustering           8.349  0.042   4.585
merge_clusters                6.961  0.023   4.966
add_cluster_annotation        5.867  0.179   5.215
split_cluster                 5.786  0.066   3.683
applySpline                   5.430  0.024   0.971
reorder_clusters_hclust       4.966  0.090   4.175
* 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 
357.840   2.537 285.213 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation5.8670.1795.215
append_ynorm0.1210.0040.049
applyMovingAverage2.4600.0241.889
applySpline5.4300.0240.971
assemble_heatmap_cluster_bars2.4180.0101.759
calc_norm_factors0.0870.0010.040
centerAtMax1.7170.0240.583
centerFixedSizeGRanges0.3230.0090.333
centerGRangesAtMax2.6390.0231.107
clusteringKmeans0.1180.0010.043
clusteringKmeansNestedHclust0.0910.0030.052
col2hex0.0020.0000.002
collapse_gr1.3360.0061.341
convert_collapsed_coord0.4120.0040.416
copy_clust_info4.7200.1163.652
crossCorrByRle0.8010.0440.846
easyLoad_FUN0.0970.0030.100
easyLoad_IDRmerged0.0810.0040.085
easyLoad_bed0.2260.0140.239
easyLoad_broadPeak0.1030.0060.108
easyLoad_narrowPeak0.0650.0010.067
easyLoad_seacr0.0670.0020.070
expandCigar0.2850.0070.271
findMaxPos0.0900.0030.053
fragLen_calcStranded3.2260.0142.626
fragLen_fromMacs2Xls0.0030.0010.004
getReadLength0.1030.0010.104
get_mapped_reads0.0160.0000.016
ggellipse1.6110.0051.616
harmonize_seqlengths0.2060.0020.208
make_clustering_matrix0.1800.0030.115
merge_clusters6.9610.0234.966
prepare_fetch_GRanges0.0320.0010.033
prepare_fetch_GRanges_names0.0930.0000.092
prepare_fetch_GRanges_width0.0340.0000.034
quantileGRangesWidth0.0030.0000.003
reorder_clusters_hclust4.9660.0904.175
reorder_clusters_manual2.8360.0102.076
reorder_clusters_stepdown3.5960.0082.735
reverse_clusters4.0910.0093.017
safeBrew0.0240.0010.025
split_cluster5.7860.0663.683
ssvAnnotateSubjectGRanges1.0980.0971.196
ssvConsensusIntervalSets0.4750.0180.493
ssvFactorizeMembTable0.0220.0020.024
ssvFeatureBars0.9730.0260.999
ssvFeatureBinaryHeatmap10.208 0.84811.056
ssvFeatureEuler1.3080.0721.380
ssvFeaturePie0.8710.0240.895
ssvFeatureUpset3.6600.0473.707
ssvFeatureVenn1.9500.0171.967
ssvFetchBam10.692 0.19910.860
ssvFetchBamPE3.3060.0953.402
ssvFetchBamPE.RNA16.980 0.025 2.322
ssvFetchBigwig1.6280.0061.634
ssvFetchGRanges0.9760.0010.977
ssvFetchSignal2.4060.0052.413
ssvMakeMembTable-methods0.9350.0170.952
ssvOverlapIntervalSets0.4480.0090.458
ssvSignalBandedQuantiles9.5670.1556.649
ssvSignalClustering8.3490.0424.585
ssvSignalHeatmap.ClusterBars11.285 0.115 6.920
ssvSignalHeatmap13.728 0.414 8.088
ssvSignalLineplot3.9720.2504.236
ssvSignalLineplotAgg1.1180.0191.082
ssvSignalScatterplot1.3920.0951.439
viewGRangesWinSample_dt1.3540.0651.413
viewGRangesWinSummary_dt2.4640.0891.700
within_clust_sort4.5080.1353.471