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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1894/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.25.0  (landing page)
Joseph R Boyd
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: 9e472c2
git_last_commit_date: 2024-04-30 11:05:16 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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 kjohnson1

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: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2024-06-11 08:19:51 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 08:29:54 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 602.5 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.25.0’
* 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 LazyData ... 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 8.656  0.594   9.345
ssvFetchBam             5.756  0.199   6.010
* 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
*** moving datasets to lazyload DB
** 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 1266 ]
> 
> proc.time()
   user  system elapsed 
253.075   5.268 260.950 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.0940.0733.180
append_ynorm0.0380.0060.043
applyMovingAverage0.6800.0480.731
applySpline0.3050.0060.313
assemble_heatmap_cluster_bars0.6770.0100.690
calc_norm_factors0.0150.0010.016
centerAtMax0.2780.0070.288
centerFixedSizeGRanges0.1680.0080.177
centerGRangesAtMax0.3340.0040.339
clusteringKmeans0.0180.0020.020
clusteringKmeansNestedHclust0.0220.0020.024
col2hex0.0010.0000.002
collapse_gr0.7130.0130.728
convert_collapsed_coord0.2250.0100.235
copy_clust_info1.5500.0111.569
crossCorrByRle0.3490.0060.356
easyLoad_FUN0.0590.0020.060
easyLoad_IDRmerged0.0430.0020.046
easyLoad_bed0.1230.0010.124
easyLoad_broadPeak0.0370.0020.039
easyLoad_narrowPeak0.0360.0010.037
easyLoad_seacr0.0420.0020.044
expandCigar0.1570.0070.165
findMaxPos0.0140.0030.018
fragLen_calcStranded1.4990.0201.538
fragLen_fromMacs2Xls0.0030.0020.004
getReadLength0.0500.0020.051
get_mapped_reads0.0110.0010.011
ggellipse0.5220.0060.530
harmonize_seqlengths0.1220.0090.131
make_clustering_matrix0.0420.0010.042
merge_clusters3.1750.0273.218
prepare_fetch_GRanges0.0300.0010.031
prepare_fetch_GRanges_names0.0810.0020.084
prepare_fetch_GRanges_width0.0260.0010.028
quantileGRangesWidth0.0010.0000.002
reorder_clusters_hclust1.7910.0121.809
reorder_clusters_manual0.9220.0140.937
reorder_clusters_stepdown1.3920.0121.464
reverse_clusters1.7400.0231.795
safeBrew0.0290.0040.034
split_cluster1.6900.0151.713
ssvConsensusIntervalSets0.3450.0090.354
ssvFactorizeMembTable0.0150.0010.017
ssvFeatureBars0.5690.0090.583
ssvFeatureBinaryHeatmap8.6560.5949.345
ssvFeatureEuler0.5270.0150.568
ssvFeaturePie0.5930.0130.608
ssvFeatureUpset2.4380.0552.503
ssvFeatureVenn0.8850.0150.907
ssvFetchBam5.7560.1996.010
ssvFetchBamPE1.8830.1222.022
ssvFetchBigwig1.0290.0131.074
ssvFetchGRanges0.7350.0040.745
ssvFetchSignal1.4470.0401.498
ssvMakeMembTable-methods0.5350.0130.549
ssvOverlapIntervalSets0.2560.0090.266
ssvSignalBandedQuantiles3.1130.0483.189
ssvSignalClustering1.7080.0251.753
ssvSignalHeatmap.ClusterBars3.0770.0513.142
ssvSignalHeatmap3.3550.0383.435
ssvSignalLineplot2.1530.0212.182
ssvSignalLineplotAgg0.7680.0110.785
ssvSignalScatterplot0.8010.0090.815
viewGRangesWinSample_dt1.1910.0321.230
viewGRangesWinSummary_dt1.1230.0341.162
within_clust_sort1.3690.0081.381