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This page was generated on 2025-03-24 11:46 -0400 (Mon, 24 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4779
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4550
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4578
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4530
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4461
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 1947/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.27.2  (landing page)
Joseph R Boyd
Snapshot Date: 2025-03-23 13:40 -0400 (Sun, 23 Mar 2025)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: ae10577
git_last_commit_date: 2024-12-09 15:04:05 -0400 (Mon, 09 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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 kjohnson3

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: 1.27.2
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_1.27.2.tar.gz
StartedAt: 2025-03-23 21:24:18 -0400 (Sun, 23 Mar 2025)
EndedAt: 2025-03-23 21:27:34 -0400 (Sun, 23 Mar 2025)
EllapsedTime: 196.4 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_1.27.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.27.2’
* 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
* 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-arm64/Resources/library’
* installing *source* package ‘seqsetvis’ ...
** this is package ‘seqsetvis’ version ‘1.27.2’
** 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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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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
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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 
100.704   4.196  79.066 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation1.2100.0571.053
append_ynorm0.0310.0030.023
applyMovingAverage0.3830.0220.215
applySpline0.2330.0180.150
assemble_heatmap_cluster_bars0.4210.0240.226
calc_norm_factors0.0220.0010.012
centerAtMax0.1660.0130.096
centerFixedSizeGRanges0.0960.0060.051
centerGRangesAtMax0.2950.0150.156
clusteringKmeans0.0220.0020.012
clusteringKmeansNestedHclust0.0240.0020.013
col2hex0.0010.0000.001
collapse_gr0.3810.0140.202
convert_collapsed_coord0.0560.0040.060
copy_clust_info0.8860.0510.503
crossCorrByRle0.1270.0060.095
easyLoad_FUN0.0150.0000.016
easyLoad_IDRmerged0.0110.0000.013
easyLoad_bed0.0360.0010.036
easyLoad_broadPeak0.0100.0000.011
easyLoad_narrowPeak0.0110.0000.011
easyLoad_seacr0.0110.0010.011
expandCigar0.0590.0040.050
findMaxPos0.0280.0040.016
fragLen_calcStranded0.6770.0220.455
fragLen_fromMacs2Xls0.0010.0010.001
getReadLength0.0300.0020.017
get_mapped_reads0.0050.0000.003
ggellipse0.2760.0090.162
harmonize_seqlengths0.0380.0040.043
make_clustering_matrix0.0490.0030.030
merge_clusters1.5290.0551.006
prepare_fetch_GRanges0.0100.0010.011
prepare_fetch_GRanges_names0.0230.0020.026
prepare_fetch_GRanges_width0.0080.0020.009
quantileGRangesWidth0.0000.0000.002
reorder_clusters_hclust0.7820.0470.588
reorder_clusters_manual0.4920.0310.317
reorder_clusters_stepdown0.7920.0400.625
reverse_clusters1.4350.0631.034
safeBrew0.0080.0010.010
split_cluster0.7400.0480.544
ssvAnnotateSubjectGRanges0.2650.0100.275
ssvConsensusIntervalSets0.0920.0040.101
ssvFactorizeMembTable0.0040.0020.006
ssvFeatureBars0.1590.0020.160
ssvFeatureBinaryHeatmap2.6120.2412.878
ssvFeatureEuler0.1650.0060.174
ssvFeaturePie0.1390.0030.144
ssvFeatureUpset0.7380.0190.757
ssvFeatureVenn0.2750.0050.281
ssvFetchBam2.2700.0821.687
ssvFetchBamPE0.6710.0270.567
ssvFetchBamPE.RNA0.7040.0420.488
ssvFetchBigwig0.9180.0610.814
ssvFetchGRanges0.2040.0090.218
ssvFetchSignal0.4200.0290.451
ssvMakeMembTable-methods0.1460.0050.151
ssvOverlapIntervalSets0.0670.0030.070
ssvSignalBandedQuantiles1.7470.1231.093
ssvSignalClustering1.4460.1320.833
ssvSignalHeatmap.ClusterBars1.6860.1400.965
ssvSignalHeatmap2.0110.1791.163
ssvSignalLineplot0.7510.0340.650
ssvSignalLineplotAgg0.4450.0270.243
ssvSignalScatterplot0.4570.0310.252
viewGRangesWinSample_dt0.5480.0210.334
viewGRangesWinSummary_dt0.4830.0320.327
within_clust_sort0.7030.0240.442