Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:16 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 palomino3


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: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 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 20.04.5 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    OK  UNNEEDED, same version is already published

Summary

Package: seqsetvis
Version: 1.16.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seqsetvis_1.16.0.tar.gz
StartedAt: 2022-10-19 04:07:47 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:16:56 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 548.8 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

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


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/seqsetvis.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 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  7.53   0.34    7.92
ssvSignalBandedQuantiles 4.97   0.14    5.12
append_ynorm             0.08   0.00    9.73
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library 'F:/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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 37 | PASS 710 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (37)

[ FAIL 0 | WARN 0 | SKIP 37 | PASS 710 ]
> 
> proc.time()
   user  system elapsed 
 197.37    3.09  200.78 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation2.420.122.77
append_ynorm0.080.009.73
applySpline0.640.072.99
assemble_heatmap_cluster_bars0.850.031.03
calc_norm_factors0.010.000.02
centerAtMax0.280.000.28
centerFixedSizeGRanges0.140.020.16
centerGRangesAtMax0.330.010.34
clusteringKmeans0.020.000.01
clusteringKmeansNestedHclust0.010.020.04
col2hex000
collapse_gr1.050.001.11
convert_collapsed_coord0.310.000.32
crossCorrByRle0.600.081.97
easyLoad_FUN0.040.000.53
easyLoad_IDRmerged0.080.010.84
easyLoad_bed0.190.020.20
easyLoad_broadPeak0.080.000.39
easyLoad_narrowPeak0.060.000.33
easyLoad_seacr0.080.000.28
expandCigar0.290.013.69
fragLen_calcStranded2.740.043.94
fragLen_fromMacs2Xls0.000.010.07
getReadLength0.080.000.14
ggellipse0.860.000.91
harmonize_seqlengths0.180.000.18
make_clustering_matrix0.020.000.02
merge_clusters3.800.024.19
prepare_fetch_GRanges0.030.000.03
prepare_fetch_GRanges_names0.130.000.13
prepare_fetch_GRanges_width0.050.000.05
quantileGRangesWidth000
reorder_clusters_hclust1.860.001.86
reorder_clusters_manual0.960.011.00
reorder_clusters_stepdown1.880.021.89
reverse_clusters3.160.063.21
safeBrew0.030.000.04
split_cluster1.680.001.68
ssvConsensusIntervalSets0.390.020.41
ssvFactorizeMembTable0.020.000.02
ssvFeatureBars0.500.030.53
ssvFeatureBinaryHeatmap7.530.347.92
ssvFeatureEuler0.500.020.51
ssvFeaturePie0.580.000.58
ssvFeatureUpset2.980.063.06
ssvFeatureVenn0.500.030.54
ssvFetchBam0.020.000.01
ssvFetchBamPE000
ssvFetchBigwig000
ssvFetchGRanges1.030.031.06
ssvFetchSignal2.170.032.21
ssvMakeMembTable-methods0.850.000.84
ssvOverlapIntervalSets0.370.000.38
ssvSignalBandedQuantiles4.970.145.12
ssvSignalClustering1.950.021.97
ssvSignalHeatmap.ClusterBars1.430.061.48
ssvSignalHeatmap1.570.031.63
ssvSignalLineplot3.220.083.30
ssvSignalLineplotAgg1.270.021.28
ssvSignalScatterplot0.830.000.84
viewGRangesWinSample_dt1.110.031.14
viewGRangesWinSummary_dt1.070.011.10
within_clust_sort1.360.041.40