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This page was generated on 2025-08-18 12:08 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1951/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-08-17 13:45 -0400 (Sun, 17 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 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: 2025-08-15 11:01:33 -0000 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 11:17:35 -0000 (Fri, 15 Aug 2025)
EllapsedTime: 961.7 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                  9.181  0.112  11.017
ssvFeatureBinaryHeatmap      7.128  0.074   7.904
ssvSignalHeatmap             5.886  0.124   6.978
ssvSignalHeatmap.ClusterBars 5.657  0.108   6.067
ssvSignalBandedQuantiles     5.517  0.159   6.257
merge_clusters               4.945  0.027   5.316
ssvSignalClustering          4.145  0.120   5.472
* 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 0 | SKIP 0 | PASS 1291 ]
> 
> proc.time()
   user  system elapsed 
386.257   1.715 453.944 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.6830.1194.590
append_ynorm0.0870.0000.089
applyMovingAverage0.9660.0080.978
applySpline0.4950.0120.510
assemble_heatmap_cluster_bars1.0980.0081.219
calc_norm_factors0.0360.0000.035
centerAtMax0.4090.0120.434
centerFixedSizeGRanges0.2690.0040.274
centerGRangesAtMax0.7360.0000.749
clusteringKmeans0.0580.0000.060
clusteringKmeansNestedHclust0.0460.0040.050
col2hex0.0010.0000.001
collapse_gr0.9970.0001.002
convert_collapsed_coord0.2680.0040.281
copy_clust_info2.4310.0152.535
crossCorrByRle0.5860.0081.147
easyLoad_FUN0.0730.0000.168
easyLoad_IDRmerged0.0610.0000.120
easyLoad_bed0.1960.0000.398
easyLoad_broadPeak0.0550.0010.106
easyLoad_narrowPeak0.0560.0040.125
easyLoad_seacr0.0630.0000.127
expandCigar0.2250.0080.446
findMaxPos0.0390.0040.043
fragLen_calcStranded2.5020.0032.891
fragLen_fromMacs2Xls0.0030.0000.009
getReadLength0.0740.0010.127
get_mapped_reads0.0110.0000.011
ggellipse0.7670.0000.826
harmonize_seqlengths0.1440.0030.168
make_clustering_matrix0.1220.0000.122
merge_clusters4.9450.0275.316
prepare_fetch_GRanges0.0440.0000.045
prepare_fetch_GRanges_names0.1320.0040.136
prepare_fetch_GRanges_width0.0430.0030.047
quantileGRangesWidth0.0040.0000.004
reorder_clusters_hclust3.1110.0004.108
reorder_clusters_manual1.6000.0001.606
reorder_clusters_stepdown3.7150.0754.007
reverse_clusters3.2160.0043.490
safeBrew0.0250.0040.028
split_cluster2.7460.0122.933
ssvAnnotateSubjectGRanges1.3620.0121.661
ssvConsensusIntervalSets0.4690.0000.943
ssvFactorizeMembTable0.0190.0000.040
ssvFeatureBars0.8010.0000.912
ssvFeatureBinaryHeatmap7.1280.0747.904
ssvFeatureEuler0.7530.0000.798
ssvFeaturePie0.6510.0000.675
ssvFeatureUpset3.5510.0004.073
ssvFeatureVenn1.3550.0081.560
ssvFetchBam 9.181 0.11211.017
ssvFetchBamPE2.8310.0993.133
ssvFetchBamPE.RNA2.2980.1632.737
ssvFetchBigwig2.1190.1072.810
ssvFetchGRanges1.1550.0631.302
ssvFetchSignal2.2680.0762.800
ssvMakeMembTable-methods0.7880.0241.156
ssvOverlapIntervalSets0.3650.0070.475
ssvSignalBandedQuantiles5.5170.1596.257
ssvSignalClustering4.1450.1205.472
ssvSignalHeatmap.ClusterBars5.6570.1086.067
ssvSignalHeatmap5.8860.1246.978
ssvSignalLineplot3.2830.0464.788
ssvSignalLineplotAgg1.0970.0041.264
ssvSignalScatterplot1.2270.0031.237
viewGRangesWinSample_dt1.8000.0282.547
viewGRangesWinSummary_dt1.7530.0122.315
within_clust_sort2.3200.0603.123