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This page was generated on 2025-08-21 12:04 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 1952/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 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: 2025-08-21 02:50:01 -0400 (Thu, 21 Aug 2025)
EndedAt: 2025-08-21 03:00:36 -0400 (Thu, 21 Aug 2025)
EllapsedTime: 634.6 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 6.893  0.396   7.290
ssvFetchBam             6.373  0.016   6.327
* 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 
268.212   1.496 264.867 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation2.9070.1052.974
append_ynorm0.0760.0000.046
applyMovingAverage0.6910.0000.680
applySpline0.3910.0030.338
assemble_heatmap_cluster_bars0.8280.0170.786
calc_norm_factors0.0370.0010.027
centerAtMax0.3090.0150.280
centerFixedSizeGRanges0.2100.0070.216
centerGRangesAtMax0.5430.0020.488
clusteringKmeans0.0380.0000.025
clusteringKmeansNestedHclust0.0410.0000.032
col2hex0.0010.0000.001
collapse_gr0.7420.0040.746
convert_collapsed_coord0.1930.0020.196
copy_clust_info1.7900.0241.727
crossCorrByRle0.4270.0110.439
easyLoad_FUN0.0530.0030.057
easyLoad_IDRmerged0.0450.0020.047
easyLoad_bed0.1340.0020.135
easyLoad_broadPeak0.0410.0000.040
easyLoad_narrowPeak0.0420.0000.041
easyLoad_seacr0.0480.0000.047
expandCigar0.1770.0040.163
findMaxPos0.0680.0010.053
fragLen_calcStranded1.5760.0001.560
fragLen_fromMacs2Xls0.0020.0000.002
getReadLength0.0540.0010.054
get_mapped_reads0.0080.0000.008
ggellipse0.5320.0030.535
harmonize_seqlengths0.1020.0010.103
make_clustering_matrix0.0800.0010.069
merge_clusters4.4270.0904.424
prepare_fetch_GRanges0.0310.0000.031
prepare_fetch_GRanges_names0.0760.0010.076
prepare_fetch_GRanges_width0.0280.0010.029
quantileGRangesWidth0.0020.0000.002
reorder_clusters_hclust1.8860.0021.843
reorder_clusters_manual1.0470.0250.994
reorder_clusters_stepdown1.9590.0011.874
reverse_clusters2.0810.0031.928
safeBrew0.0200.0020.022
split_cluster1.8100.0151.702
ssvAnnotateSubjectGRanges1.0700.0081.079
ssvConsensusIntervalSets0.3260.0050.332
ssvFactorizeMembTable0.0150.0000.015
ssvFeatureBars0.5870.0080.596
ssvFeatureBinaryHeatmap6.8930.3967.290
ssvFeatureEuler0.5560.0000.557
ssvFeaturePie0.4940.0020.496
ssvFeatureUpset2.4680.0012.471
ssvFeatureVenn0.9130.0040.918
ssvFetchBam6.3730.0166.327
ssvFetchBamPE2.1050.0012.105
ssvFetchBamPE.RNA1.6170.0271.576
ssvFetchBigwig1.4620.0081.472
ssvFetchGRanges0.7970.0020.799
ssvFetchSignal1.5070.0031.511
ssvMakeMembTable-methods0.5880.0010.590
ssvOverlapIntervalSets0.2540.0150.268
ssvSignalBandedQuantiles4.1000.2484.156
ssvSignalClustering2.9520.2403.045
ssvSignalHeatmap.ClusterBars3.5570.1833.562
ssvSignalHeatmap4.3400.1854.154
ssvSignalLineplot2.3180.0612.366
ssvSignalLineplotAgg0.8020.0150.800
ssvSignalScatterplot0.9400.0490.939
viewGRangesWinSample_dt1.2140.0461.255
viewGRangesWinSummary_dt1.1570.0031.134
within_clust_sort1.5830.0411.557