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This page was generated on 2024-10-05 11:44 -0400 (Sat, 05 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4461
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4466
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4498
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4446
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4445
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 1914/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.25.4  (landing page)
Joseph R Boyd
Snapshot Date: 2024-10-04 13:40 -0400 (Fri, 04 Oct 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: 0e66de9
git_last_commit_date: 2024-09-13 10:52:02 -0400 (Fri, 13 Sep 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.25.4
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_1.25.4.tar.gz
StartedAt: 2024-10-05 00:20:49 -0400 (Sat, 05 Oct 2024)
EndedAt: 2024-10-05 00:23:58 -0400 (Sat, 05 Oct 2024)
EllapsedTime: 189.2 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_1.25.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.25.4’
* 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/4.4-arm64/Resources/library’
* installing *source* package ‘seqsetvis’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 1284 ]
> 
> proc.time()
   user  system elapsed 
 99.403   2.759  76.332 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation1.2060.0351.010
append_ynorm0.0390.0040.029
applyMovingAverage0.3950.0170.206
applySpline0.1980.0090.106
assemble_heatmap_cluster_bars0.4140.0130.214
calc_norm_factors0.0200.0010.011
centerAtMax0.1580.0060.082
centerFixedSizeGRanges0.0870.0050.046
centerGRangesAtMax0.2240.0100.117
clusteringKmeans0.0230.0020.013
clusteringKmeansNestedHclust0.0250.0020.013
col2hex0.0010.0000.001
collapse_gr0.3880.0130.207
convert_collapsed_coord0.0530.0030.056
copy_clust_info0.8910.0250.463
crossCorrByRle0.1370.0040.099
easyLoad_FUN0.0400.0020.042
easyLoad_IDRmerged0.0130.0010.013
easyLoad_bed0.0360.0000.036
easyLoad_broadPeak0.0100.0010.010
easyLoad_narrowPeak0.010.000.01
easyLoad_seacr0.0110.0010.011
expandCigar0.0570.0030.047
findMaxPos0.0280.0040.015
fragLen_calcStranded0.6840.0160.445
fragLen_fromMacs2Xls0.0020.0000.002
getReadLength0.0330.0020.017
get_mapped_reads0.0060.0010.002
ggellipse0.2670.0070.153
harmonize_seqlengths0.0380.0030.042
make_clustering_matrix0.0440.0020.026
merge_clusters1.4950.0350.950
prepare_fetch_GRanges0.0080.0010.009
prepare_fetch_GRanges_names0.0220.0010.023
prepare_fetch_GRanges_width0.0080.0010.009
quantileGRangesWidth0.0010.0000.001
reorder_clusters_hclust0.7800.0150.535
reorder_clusters_manual0.5230.0140.297
reorder_clusters_stepdown0.7980.0140.566
reverse_clusters0.8920.0270.603
safeBrew0.0080.0010.010
split_cluster0.8700.0230.558
ssvAnnotateSubjectGRanges0.2730.0070.281
ssvConsensusIntervalSets0.0970.0030.100
ssvFactorizeMembTable0.0050.0010.005
ssvFeatureBars0.1660.0020.168
ssvFeatureBinaryHeatmap2.7590.1752.945
ssvFeatureEuler0.1540.0030.157
ssvFeaturePie0.1460.0120.157
ssvFeatureUpset0.7090.0120.722
ssvFeatureVenn0.2520.0020.255
ssvFetchBam2.3150.0831.718
ssvFetchBamPE0.6790.0250.565
ssvFetchBamPE.RNA0.6590.0360.442
ssvFetchBigwig0.5700.0130.385
ssvFetchGRanges0.2100.0010.212
ssvFetchSignal0.4170.0100.426
ssvMakeMembTable-methods0.1450.0050.151
ssvOverlapIntervalSets0.0670.0050.071
ssvSignalBandedQuantiles1.8400.0821.085
ssvSignalClustering1.5170.0740.815
ssvSignalHeatmap.ClusterBars1.7550.0650.922
ssvSignalHeatmap2.1100.0841.098
ssvSignalLineplot0.8250.0540.712
ssvSignalLineplotAgg0.4280.0170.222
ssvSignalScatterplot0.4980.0180.259
viewGRangesWinSample_dt0.5800.0170.350
viewGRangesWinSummary_dt0.4940.0130.324
within_clust_sort0.6900.0180.427