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This page was generated on 2025-10-08 12:54 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 Oct 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  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for seqsetvis on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: seqsetvis
Version: 1.29.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqsetvis_1.29.1.tar.gz
StartedAt: 2025-10-07 12:05:45 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 12:19:37 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 831.1 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqsetvis_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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
ssvFetchBam                  9.405  0.019   9.452
ssvFeatureBinaryHeatmap      7.108  0.124   7.257
ssvSignalHeatmap             6.975  0.031   7.022
merge_clusters               6.425  0.043   6.491
ssvSignalHeatmap.ClusterBars 6.080  0.036   6.131
ssvSignalBandedQuantiles     5.973  0.016   6.055
ssvSignalClustering          5.596  0.052   5.660
add_cluster_annotation       4.783  0.208   5.045
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
396.936   1.854 399.790 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation4.7830.2085.045
append_ynorm0.0870.0000.088
applyMovingAverage1.4350.0801.519
applySpline0.6490.0040.652
assemble_heatmap_cluster_bars1.4150.0121.426
calc_norm_factors0.0320.0000.031
centerAtMax0.3790.0040.382
centerFixedSizeGRanges0.2070.0040.212
centerGRangesAtMax0.7180.0080.724
clusteringKmeans0.0360.0000.033
clusteringKmeansNestedHclust0.0410.0000.040
col2hex0.0010.0000.001
collapse_gr0.9840.0161.002
convert_collapsed_coord0.3380.0080.347
copy_clust_info2.5740.0722.648
crossCorrByRle0.6050.0160.626
easyLoad_FUN0.0690.0040.074
easyLoad_IDRmerged0.0550.0040.061
easyLoad_bed0.1680.0000.168
easyLoad_broadPeak0.0480.0000.049
easyLoad_narrowPeak0.0500.0000.051
easyLoad_seacr0.0580.0000.059
expandCigar0.2140.0040.220
findMaxPos0.0420.0000.042
fragLen_calcStranded2.6350.0082.650
fragLen_fromMacs2Xls0.0030.0000.004
getReadLength0.0770.0000.078
get_mapped_reads0.0100.0000.011
ggellipse1.2490.0041.256
harmonize_seqlengths0.160.000.16
make_clustering_matrix0.1230.0000.123
merge_clusters6.4250.0436.491
prepare_fetch_GRanges0.0490.0040.053
prepare_fetch_GRanges_names0.1280.0040.133
prepare_fetch_GRanges_width0.0420.0040.047
quantileGRangesWidth0.0000.0040.004
reorder_clusters_hclust3.7450.0203.809
reorder_clusters_manual1.9980.0282.031
reorder_clusters_stepdown4.4600.1554.629
reverse_clusters3.8040.0163.830
safeBrew0.0270.0020.030
split_cluster3.3400.0293.372
ssvAnnotateSubjectGRanges1.4350.0121.450
ssvConsensusIntervalSets0.4480.0040.454
ssvFactorizeMembTable0.0190.0000.019
ssvFeatureBars1.3060.0081.317
ssvFeatureBinaryHeatmap7.1080.1247.257
ssvFeatureEuler1.2620.0001.266
ssvFeaturePie0.9470.0000.950
ssvFeatureUpset4.8440.0284.886
ssvFeatureVenn2.2440.0002.250
ssvFetchBam9.4050.0199.452
ssvFetchBamPE2.7920.0552.860
ssvFetchBamPE.RNA2.2160.0002.221
ssvFetchBigwig1.9910.0001.998
ssvFetchGRanges1.1370.0721.212
ssvFetchSignal2.2370.0122.255
ssvMakeMembTable-methods0.7770.0000.779
ssvOverlapIntervalSets0.3470.0000.348
ssvSignalBandedQuantiles5.9730.0166.055
ssvSignalClustering5.5960.0525.660
ssvSignalHeatmap.ClusterBars6.0800.0366.131
ssvSignalHeatmap6.9750.0317.022
ssvSignalLineplot4.3560.0044.373
ssvSignalLineplotAgg1.4680.0201.492
ssvSignalScatterplot1.6160.0201.636
viewGRangesWinSample_dt1.7380.0041.748
viewGRangesWinSummary_dt1.6410.0041.650
within_clust_sort2.7220.0132.733