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This page was generated on 2024-06-27 11:39 -0400 (Thu, 27 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4691
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4405
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4354
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 1897/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.25.2  (landing page)
Joseph R Boyd
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: ced4a49
git_last_commit_date: 2024-05-28 14:47:09 -0400 (Tue, 28 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.25.2
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_1.25.2.tar.gz
StartedAt: 2024-06-26 23:38:11 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 23:41:07 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 175.9 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_1.25.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.25.2’
* 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/4.4-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 RC (2024-06-06 r86719) -- "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 
 68.874   1.496  70.397 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation0.8730.0160.889
append_ynorm0.0150.0030.017
applyMovingAverage0.1870.0120.199
applySpline0.0860.0010.087
assemble_heatmap_cluster_bars0.1780.0020.181
calc_norm_factors0.0080.0010.009
centerAtMax0.0740.0020.075
centerFixedSizeGRanges0.0360.0020.038
centerGRangesAtMax0.0940.0020.096
clusteringKmeans0.0090.0010.011
clusteringKmeansNestedHclust0.0100.0020.012
col2hex0.0010.0000.000
collapse_gr0.1700.0030.174
convert_collapsed_coord0.0430.0020.044
copy_clust_info0.3980.0030.402
crossCorrByRle0.0930.0020.095
easyLoad_FUN0.0170.0010.018
easyLoad_IDRmerged0.0140.0010.015
easyLoad_bed0.0360.0000.037
easyLoad_broadPeak0.0090.0010.010
easyLoad_narrowPeak0.010.000.01
easyLoad_seacr0.0110.0000.012
expandCigar0.0450.0040.048
findMaxPos0.0130.0020.014
fragLen_calcStranded0.4130.0060.419
fragLen_fromMacs2Xls0.0010.0000.001
getReadLength0.0140.0010.015
get_mapped_reads0.0020.0000.002
ggellipse0.1370.0020.138
harmonize_seqlengths0.0280.0030.030
make_clustering_matrix0.0170.0010.018
merge_clusters0.8870.0100.898
prepare_fetch_GRanges0.0080.0010.009
prepare_fetch_GRanges_names0.0210.0010.022
prepare_fetch_GRanges_width0.0070.0010.009
quantileGRangesWidth0.0010.0000.001
reorder_clusters_hclust0.5270.0040.532
reorder_clusters_manual0.2810.0050.286
reorder_clusters_stepdown0.5230.0030.528
reverse_clusters0.6080.0180.626
safeBrew0.0090.0020.010
split_cluster0.7680.0120.780
ssvAnnotateSubjectGRanges0.2280.0050.233
ssvConsensusIntervalSets0.0810.0030.085
ssvFactorizeMembTable0.0040.0010.005
ssvFeatureBars0.1340.0010.135
ssvFeatureBinaryHeatmap2.3540.1662.522
ssvFeatureEuler0.1570.0020.162
ssvFeaturePie0.1370.0080.145
ssvFeatureUpset0.7160.0050.721
ssvFeatureVenn0.2600.0030.262
ssvFetchBam1.5760.0611.637
ssvFetchBamPE0.5260.0330.566
ssvFetchBamPE.RNA0.3960.0130.409
ssvFetchBigwig0.3770.0070.384
ssvFetchGRanges0.1780.0010.179
ssvFetchSignal0.3600.0160.375
ssvMakeMembTable-methods0.1310.0040.135
ssvOverlapIntervalSets0.0620.0030.065
ssvSignalBandedQuantiles0.9450.0160.962
ssvSignalClustering0.6340.0060.640
ssvSignalHeatmap.ClusterBars0.8390.0160.856
ssvSignalHeatmap0.9660.0090.978
ssvSignalLineplot0.5900.0030.594
ssvSignalLineplotAgg0.2310.0030.235
ssvSignalScatterplot0.2440.0040.248
viewGRangesWinSample_dt0.3370.0090.346
viewGRangesWinSummary_dt0.3070.0030.311
within_clust_sort0.3850.0060.391