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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1934/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.26.0  (landing page)
Joseph R Boyd
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_20
git_last_commit: 31e216f
git_last_commit_date: 2024-10-29 10:27:03 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (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
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


CHECK results for seqsetvis on merida1

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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2024-12-20 09:35:23 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 09:57:28 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1325.5 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 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 ‘1.26.0’
* 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 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                  15.087  0.463  15.982
ssvFeatureBinaryHeatmap       9.332  0.858  10.612
ssvSignalHeatmap              9.457  0.280  10.158
ssvSignalBandedQuantiles      9.475  0.130   9.669
merge_clusters                7.979  0.086   8.058
ssvSignalHeatmap.ClusterBars  7.823  0.120   7.899
ssvSignalClustering           6.219  0.098   6.486
reverse_clusters              5.959  0.123   6.153
add_cluster_annotation        5.792  0.196   6.309
ssvFeatureUpset               5.857  0.048   6.137
ssvSignalLineplot             5.145  0.035   5.340
split_cluster                 5.026  0.101   4.303
* 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-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 1284 ]
> 
> proc.time()
   user  system elapsed 
632.105  11.714 643.425 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation5.7920.1966.309
append_ynorm0.1010.0210.168
applyMovingAverage1.6790.1711.938
applySpline0.7280.0200.750
assemble_heatmap_cluster_bars1.7340.0271.760
calc_norm_factors0.0520.0040.057
centerAtMax0.6360.0290.649
centerFixedSizeGRanges0.2850.0160.296
centerGRangesAtMax0.9840.0280.879
clusteringKmeans0.0560.0100.065
clusteringKmeansNestedHclust0.0700.0120.081
col2hex0.0020.0000.002
collapse_gr1.6190.0291.800
convert_collapsed_coord0.4360.0160.462
copy_clust_info3.8690.0574.116
crossCorrByRle0.7380.0150.761
easyLoad_FUN0.1110.0020.118
easyLoad_IDRmerged0.0920.0040.096
easyLoad_bed0.3150.0040.323
easyLoad_broadPeak0.0810.0020.089
easyLoad_narrowPeak0.0820.0030.085
easyLoad_seacr0.0950.0030.099
expandCigar0.3510.0330.387
findMaxPos0.0700.0190.087
fragLen_calcStranded4.0920.0694.150
fragLen_fromMacs2Xls0.0040.0010.005
getReadLength0.1210.0110.136
get_mapped_reads0.0180.0020.020
ggellipse1.2760.0101.302
harmonize_seqlengths0.1930.0140.209
make_clustering_matrix0.2130.0110.220
merge_clusters7.9790.0868.058
prepare_fetch_GRanges0.0710.0040.078
prepare_fetch_GRanges_names0.1880.0070.198
prepare_fetch_GRanges_width0.0670.0050.073
quantileGRangesWidth0.0040.0030.008
reorder_clusters_hclust4.6140.0434.676
reorder_clusters_manual2.4210.0302.455
reorder_clusters_stepdown4.6000.0334.656
reverse_clusters5.9590.1236.153
safeBrew0.0430.0050.089
split_cluster5.0260.1014.303
ssvAnnotateSubjectGRanges2.2390.0572.320
ssvConsensusIntervalSets0.7140.0150.744
ssvFactorizeMembTable0.0330.0100.042
ssvFeatureBars1.2180.0111.243
ssvFeatureBinaryHeatmap 9.332 0.85810.612
ssvFeatureEuler1.2230.0201.380
ssvFeaturePie1.0910.0301.146
ssvFeatureUpset5.8570.0486.137
ssvFeatureVenn2.1280.0202.215
ssvFetchBam15.087 0.46315.982
ssvFetchBamPE4.5660.2774.946
ssvFetchBamPE.RNA3.3000.0713.679
ssvFetchBigwig3.2860.0753.385
ssvFetchGRanges1.7560.0261.793
ssvFetchSignal3.4800.0913.624
ssvMakeMembTable-methods1.1640.0161.220
ssvOverlapIntervalSets0.5100.0150.529
ssvSignalBandedQuantiles9.4750.1309.669
ssvSignalClustering6.2190.0986.486
ssvSignalHeatmap.ClusterBars7.8230.1207.899
ssvSignalHeatmap 9.457 0.28010.158
ssvSignalLineplot5.1450.0355.340
ssvSignalLineplotAgg1.9020.0301.889
ssvSignalScatterplot1.9850.0352.539
viewGRangesWinSample_dt2.9980.0833.125
viewGRangesWinSummary_dt2.8790.0962.989
within_clust_sort3.5370.0573.612