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This page was generated on 2025-08-04 11:48 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1.28.0  (landing page)
Joseph R Boyd
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_21
git_last_commit: 28d6e95
git_last_commit_date: 2025-04-15 11:20:09 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for seqsetvis on kunpeng2

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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2025-08-01 14:38:25 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 14:53:19 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 894.4 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.28.0’
* 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              8.944  0.024   9.943
ssvFeatureBinaryHeatmap  8.791  0.107  10.330
ssvSignalHeatmap         5.660  0.052   5.953
ssvSignalBandedQuantiles 5.171  0.004   5.382
merge_clusters           5.125  0.012   5.316
add_cluster_annotation   4.034  0.204   5.052
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘seqsetvis’ ...
** this is package ‘seqsetvis’ version ‘1.28.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 
373.735   1.477 412.442 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation4.0340.2045.052
append_ynorm0.0860.0040.090
applyMovingAverage0.9860.0161.475
applySpline0.4710.0000.472
assemble_heatmap_cluster_bars1.0810.0041.088
calc_norm_factors0.0360.0000.036
centerAtMax0.3820.0040.386
centerFixedSizeGRanges0.1980.0040.202
centerGRangesAtMax0.7380.0320.774
clusteringKmeans0.0560.0040.062
clusteringKmeansNestedHclust0.0500.0000.051
col2hex0.0010.0000.001
collapse_gr1.0010.0001.208
convert_collapsed_coord0.2740.0000.274
copy_clust_info2.3530.0512.426
crossCorrByRle0.4340.0040.552
easyLoad_FUN0.0720.0040.152
easyLoad_IDRmerged0.0590.0000.063
easyLoad_bed0.1810.0000.181
easyLoad_broadPeak0.0480.0000.092
easyLoad_narrowPeak0.0500.0000.097
easyLoad_seacr0.0550.0000.108
expandCigar0.2120.0090.456
findMaxPos0.0420.0040.094
fragLen_calcStranded2.4390.0242.836
fragLen_fromMacs2Xls0.0030.0000.009
getReadLength0.0740.0000.107
get_mapped_reads0.0110.0000.011
ggellipse0.7790.0000.782
harmonize_seqlengths0.1500.0040.156
make_clustering_matrix0.1270.0000.127
merge_clusters5.1250.0125.316
prepare_fetch_GRanges0.0400.0000.041
prepare_fetch_GRanges_names0.110.000.11
prepare_fetch_GRanges_width0.0410.0000.041
quantileGRangesWidth0.0030.0000.004
reorder_clusters_hclust2.8830.0123.097
reorder_clusters_manual1.4930.0121.577
reorder_clusters_stepdown2.9510.0043.507
reverse_clusters3.1760.0203.291
safeBrew0.0540.0000.053
split_cluster2.6790.0023.487
ssvAnnotateSubjectGRanges2.3910.0842.894
ssvConsensusIntervalSets0.4380.0350.783
ssvFactorizeMembTable0.020.000.04
ssvFeatureBars0.7610.0080.954
ssvFeatureBinaryHeatmap 8.791 0.10710.330
ssvFeatureEuler0.7270.0040.784
ssvFeaturePie0.6210.0000.642
ssvFeatureUpset3.5370.0003.584
ssvFeatureVenn1.3330.0001.480
ssvFetchBam8.9440.0249.943
ssvFetchBamPE2.6930.0072.853
ssvFetchBamPE.RNA2.1610.0002.344
ssvFetchBigwig1.9830.0202.028
ssvFetchGRanges1.0880.0001.094
ssvFetchSignal2.1000.0112.136
ssvMakeMembTable-methods0.7230.0080.742
ssvOverlapIntervalSets0.3440.0040.536
ssvSignalBandedQuantiles5.1710.0045.382
ssvSignalClustering3.9990.0124.174
ssvSignalHeatmap.ClusterBars4.6360.0004.774
ssvSignalHeatmap5.6600.0525.953
ssvSignalLineplot3.2520.0003.651
ssvSignalLineplotAgg1.1000.0001.128
ssvSignalScatterplot1.2110.0041.218
viewGRangesWinSample_dt1.7020.0001.767
viewGRangesWinSummary_dt1.6910.0042.044
within_clust_sort2.1830.0042.229