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This page was generated on 2025-08-30 12:06 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1954/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.29.1  (landing page)
Joseph R Boyd
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 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: 2025-08-29 23:47:27 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 23:58:24 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 656.9 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 (2025-06-13)
* 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 7.389  0.659   8.122
ssvFetchBam             6.780  0.305   7.121
* 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 (2025-06-13) -- "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 0 | SKIP 0 | PASS 1291 ]
> 
> proc.time()
   user  system elapsed 
296.744   6.786 305.390 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.0910.0913.196
append_ynorm0.0550.0060.062
applyMovingAverage0.7350.0120.751
applySpline0.3630.0090.373
assemble_heatmap_cluster_bars0.8020.0110.816
calc_norm_factors0.0260.0030.031
centerAtMax0.2850.0060.292
centerFixedSizeGRanges0.1960.0090.206
centerGRangesAtMax0.5780.0200.601
clusteringKmeans0.0310.0030.033
clusteringKmeansNestedHclust0.0380.0040.043
col2hex0.0010.0010.001
collapse_gr0.8140.0300.849
convert_collapsed_coord0.2480.0120.260
copy_clust_info1.8310.0461.920
crossCorrByRle0.4800.0160.504
easyLoad_FUN0.0540.0010.056
easyLoad_IDRmerged0.0460.0020.049
easyLoad_bed0.1490.0020.151
easyLoad_broadPeak0.0480.0020.049
easyLoad_narrowPeak0.0480.0020.050
easyLoad_seacr0.0440.0020.046
expandCigar0.1850.0190.205
findMaxPos0.0370.0090.046
fragLen_calcStranded1.7600.0371.806
fragLen_fromMacs2Xls0.0020.0010.003
getReadLength0.0650.0080.072
get_mapped_reads0.0110.0010.012
ggellipse0.6200.0060.630
harmonize_seqlengths0.1580.0110.170
make_clustering_matrix0.0790.0040.084
merge_clusters3.6100.0313.655
prepare_fetch_GRanges0.0350.0020.038
prepare_fetch_GRanges_names0.0910.0020.094
prepare_fetch_GRanges_width0.0360.0020.039
quantileGRangesWidth0.0030.0020.005
reorder_clusters_hclust2.2320.0272.272
reorder_clusters_manual1.2530.0121.271
reorder_clusters_stepdown2.2460.0202.281
reverse_clusters3.0840.0403.144
safeBrew0.0230.0040.028
split_cluster1.8810.0451.953
ssvAnnotateSubjectGRanges1.0810.0231.110
ssvConsensusIntervalSets0.3770.0110.391
ssvFactorizeMembTable0.0130.0020.016
ssvFeatureBars0.6550.0090.669
ssvFeatureBinaryHeatmap7.3890.6598.122
ssvFeatureEuler0.6000.0140.618
ssvFeaturePie0.5620.0270.593
ssvFeatureUpset2.7600.0322.809
ssvFeatureVenn1.0290.0141.050
ssvFetchBam6.7800.3057.121
ssvFetchBamPE2.3780.1892.592
ssvFetchBamPE.RNA1.7980.0761.905
ssvFetchBigwig1.7180.0461.786
ssvFetchGRanges0.8820.0110.900
ssvFetchSignal1.7770.0621.851
ssvMakeMembTable-methods0.6490.0160.671
ssvOverlapIntervalSets0.2970.0130.313
ssvSignalBandedQuantiles4.0510.0744.168
ssvSignalClustering2.9340.0603.026
ssvSignalHeatmap.ClusterBars4.6240.1234.789
ssvSignalHeatmap4.3030.1184.460
ssvSignalLineplot2.3720.0232.412
ssvSignalLineplotAgg0.8490.0120.868
ssvSignalScatterplot0.9820.0171.007
viewGRangesWinSample_dt1.3780.0591.450
viewGRangesWinSummary_dt1.2510.0601.319
within_clust_sort1.6810.0311.724