Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:23 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for seqsetvis on nebbiolo1


To the developers/maintainers of the seqsetvis package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1819/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.16.0  (landing page)
Joseph R Boyd
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_15
git_last_commit: e3338b3
git_last_commit_date: 2022-04-26 11:48:16 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: seqsetvis
Version: 1.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings seqsetvis_1.16.0.tar.gz
StartedAt: 2022-06-23 22:00:07 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 22:08:22 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 494.8 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings seqsetvis_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/seqsetvis.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.16.0’
* 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 R 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 7.063  0.416   7.479
ssvFetchBam             6.187  0.059   6.210
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 1176 ]
> 
> proc.time()
   user  system elapsed 
224.404   2.528 223.575 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation1.8000.0631.825
append_ynorm0.0760.0000.046
applySpline0.4100.0000.373
assemble_heatmap_cluster_bars0.5490.0120.530
calc_norm_factors0.0210.0000.012
centerAtMax0.3450.0170.303
centerFixedSizeGRanges0.1710.0000.171
centerGRangesAtMax0.3560.0030.314
clusteringKmeans0.0260.0000.015
clusteringKmeansNestedHclust0.0310.0000.022
col2hex0.0010.0000.001
collapse_gr0.6330.0120.645
convert_collapsed_coord0.2280.0000.227
crossCorrByRle0.3570.0000.357
easyLoad_FUN0.0480.0000.047
easyLoad_IDRmerged0.0530.0040.056
easyLoad_bed0.1730.0000.173
easyLoad_broadPeak0.0340.0040.039
easyLoad_narrowPeak0.0340.0040.038
easyLoad_seacr0.0300.0040.035
expandCigar0.1790.0080.167
fragLen_calcStranded1.5570.0161.559
fragLen_fromMacs2Xls0.0020.0000.003
getReadLength0.0520.0000.052
ggellipse0.4970.0040.501
harmonize_seqlengths0.0930.0040.097
make_clustering_matrix0.0100.0020.007
merge_clusters2.6570.0482.621
prepare_fetch_GRanges0.0290.0000.029
prepare_fetch_GRanges_names0.0800.0080.088
prepare_fetch_GRanges_width0.0230.0040.027
quantileGRangesWidth0.0020.0000.002
reorder_clusters_hclust2.5600.0402.553
reorder_clusters_manual0.7810.0200.761
reorder_clusters_stepdown1.4500.0121.425
reverse_clusters1.5640.0041.497
safeBrew0.0230.0000.022
split_cluster1.3690.0281.331
ssvConsensusIntervalSets0.3800.0160.395
ssvFactorizeMembTable0.0150.0000.015
ssvFeatureBars0.5430.0120.555
ssvFeatureBinaryHeatmap7.0630.4167.479
ssvFeatureEuler0.4380.0040.442
ssvFeaturePie0.5180.0080.526
ssvFeatureUpset2.1240.0082.133
ssvFeatureVenn0.4710.0040.474
ssvFetchBam6.1870.0596.210
ssvFetchBamPE1.9950.0162.013
ssvFetchBigwig1.4020.0521.454
ssvFetchGRanges0.7210.0080.729
ssvFetchSignal1.4150.0081.424
ssvMakeMembTable-methods0.5250.0210.546
ssvOverlapIntervalSets0.2520.0000.252
ssvSignalBandedQuantiles4.4250.0204.325
ssvSignalClustering1.6890.0001.620
ssvSignalHeatmap.ClusterBars1.5670.0041.472
ssvSignalHeatmap1.5300.0121.469
ssvSignalLineplot2.0700.0042.069
ssvSignalLineplotAgg1.0950.0031.078
ssvSignalScatterplot0.8830.0160.845
viewGRangesWinSample_dt1.2550.0081.249
viewGRangesWinSummary_dt1.2440.0041.220
within_clust_sort1.1290.0121.097