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This page was generated on 2025-09-29 12:05 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1964/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.29.1.tar.gz
StartedAt: 2025-09-29 00:15:30 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 00:27:10 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 700.1 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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  8.080  0.731   8.885
ssvFetchBam              7.129  0.400   7.599
ssvSignalHeatmap         5.552  0.127   5.721
merge_clusters           4.988  0.052   5.073
ssvSignalBandedQuantiles 4.945  0.071   5.066
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

seqsetvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
307.879   7.398 317.239 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.9810.1024.105
append_ynorm0.0530.0060.059
applyMovingAverage1.1240.0231.164
applySpline0.5490.0240.585
assemble_heatmap_cluster_bars1.1280.0241.177
calc_norm_factors0.0270.0030.031
centerAtMax0.3120.0070.322
centerFixedSizeGRanges0.2040.0110.216
centerGRangesAtMax0.6350.0160.653
clusteringKmeans0.0290.0050.034
clusteringKmeansNestedHclust0.0330.0060.039
col2hex0.0010.0000.001
collapse_gr0.8270.0150.846
convert_collapsed_coord0.2780.0140.293
copy_clust_info2.1080.0232.144
crossCorrByRle0.5030.0150.523
easyLoad_FUN0.0630.0010.065
easyLoad_IDRmerged0.0500.0020.053
easyLoad_bed0.1530.0020.156
easyLoad_broadPeak0.0690.0020.071
easyLoad_narrowPeak0.0470.0020.048
easyLoad_seacr0.0480.0020.050
expandCigar0.1800.0190.201
findMaxPos0.0380.0080.047
fragLen_calcStranded1.9390.0441.997
fragLen_fromMacs2Xls0.0020.0010.004
getReadLength0.0650.0110.076
get_mapped_reads0.0100.0010.011
ggellipse0.9690.0160.992
harmonize_seqlengths0.1460.0110.158
make_clustering_matrix0.0710.0030.074
merge_clusters4.9880.0525.073
prepare_fetch_GRanges0.0340.0020.036
prepare_fetch_GRanges_names0.0950.0040.098
prepare_fetch_GRanges_width0.0370.0020.039
quantileGRangesWidth0.0040.0010.005
reorder_clusters_hclust3.5800.0613.709
reorder_clusters_manual1.5190.0161.548
reorder_clusters_stepdown2.6940.0252.739
reverse_clusters2.9510.0363.013
safeBrew0.0220.0040.028
split_cluster2.5480.0212.585
ssvAnnotateSubjectGRanges1.1230.0321.164
ssvConsensusIntervalSets0.3790.0110.392
ssvFactorizeMembTable0.0160.0050.021
ssvFeatureBars0.9080.0070.920
ssvFeatureBinaryHeatmap8.0800.7318.885
ssvFeatureEuler0.9760.0271.013
ssvFeaturePie0.7860.0340.855
ssvFeatureUpset4.0590.0634.170
ssvFeatureVenn1.7800.0241.822
ssvFetchBam7.1290.4007.599
ssvFetchBamPE2.4030.2922.733
ssvFetchBamPE.RNA1.8300.0531.901
ssvFetchBigwig1.6410.0271.684
ssvFetchGRanges0.9400.0220.968
ssvFetchSignal1.8380.0711.928
ssvMakeMembTable-methods0.6790.0140.699
ssvOverlapIntervalSets0.3080.0120.321
ssvSignalBandedQuantiles4.9450.0715.066
ssvSignalClustering3.6920.0613.779
ssvSignalHeatmap.ClusterBars4.9100.0514.990
ssvSignalHeatmap5.5520.1275.721
ssvSignalLineplot3.6410.0443.724
ssvSignalLineplotAgg1.1670.0111.184
ssvSignalScatterplot1.3460.0161.368
viewGRangesWinSample_dt1.4080.0441.458
viewGRangesWinSummary_dt1.3930.0791.479
within_clust_sort2.1360.0322.178