Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:08:09 -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 merida1


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: /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_1.16.0.tar.gz
StartedAt: 2022-06-24 08:48:36 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 09:10:16 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 1299.8 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/seqsetvis.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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
ssvFetchBam              14.630  0.374  19.703
ssvSignalBandedQuantiles 10.738  0.069  14.258
ssvFeatureBinaryHeatmap   9.545  0.656  13.356
merge_clusters            5.982  0.047   7.645
ssvFeatureUpset           5.022  0.025   6.469
ssvSignalLineplot         4.793  0.016   6.231
ssvFetchBamPE             4.332  0.300   5.708
reorder_clusters_hclust   4.137  0.027   5.129
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
512.953   7.105 616.539 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.1810.1253.890
append_ynorm0.0580.0030.074
applySpline0.9240.0111.096
assemble_heatmap_cluster_bars1.2120.0101.420
calc_norm_factors0.0250.0010.027
centerAtMax0.5960.0100.707
centerFixedSizeGRanges0.3000.0110.362
centerGRangesAtMax0.7380.0040.871
clusteringKmeans0.0260.0020.034
clusteringKmeansNestedHclust0.0420.0020.050
col2hex0.0020.0000.002
collapse_gr1.4210.0151.680
convert_collapsed_coord0.4160.0100.501
crossCorrByRle0.7970.0110.967
easyLoad_FUN0.0990.0070.125
easyLoad_IDRmerged0.1790.0060.236
easyLoad_bed0.2710.0010.337
easyLoad_broadPeak0.0800.0020.100
easyLoad_narrowPeak0.0790.0010.094
easyLoad_seacr0.0700.0020.084
expandCigar0.3270.0200.415
fragLen_calcStranded3.9030.0434.799
fragLen_fromMacs2Xls0.0030.0000.004
getReadLength0.1090.0080.141
ggellipse1.1190.0081.428
harmonize_seqlengths0.2050.0100.274
make_clustering_matrix0.0110.0010.013
merge_clusters5.9820.0477.645
prepare_fetch_GRanges0.0620.0010.084
prepare_fetch_GRanges_names0.1700.0030.216
prepare_fetch_GRanges_width0.0820.0020.111
quantileGRangesWidth0.0020.0000.003
reorder_clusters_hclust4.1370.0275.129
reorder_clusters_manual1.6460.0242.054
reorder_clusters_stepdown3.3200.0144.107
reverse_clusters3.3760.0144.301
safeBrew0.0430.0020.056
split_cluster2.8880.0133.636
ssvConsensusIntervalSets0.7760.0110.990
ssvFactorizeMembTable0.0240.0010.033
ssvFeatureBars1.1950.0051.520
ssvFeatureBinaryHeatmap 9.545 0.65613.356
ssvFeatureEuler1.0270.0111.372
ssvFeaturePie1.0760.0241.480
ssvFeatureUpset5.0220.0256.469
ssvFeatureVenn1.0440.0071.347
ssvFetchBam14.630 0.37419.703
ssvFetchBamPE4.3320.3005.708
ssvFetchBigwig3.1650.0303.976
ssvFetchGRanges1.7230.0092.282
ssvFetchSignal3.4730.0694.667
ssvMakeMembTable-methods1.1560.0131.540
ssvOverlapIntervalSets0.5130.0100.687
ssvSignalBandedQuantiles10.738 0.06914.258
ssvSignalClustering3.5660.0174.852
ssvSignalHeatmap.ClusterBars3.2630.0134.318
ssvSignalHeatmap3.3510.0164.298
ssvSignalLineplot4.7930.0166.231
ssvSignalLineplotAgg2.2960.0112.999
ssvSignalScatterplot1.6180.0082.136
viewGRangesWinSample_dt2.8910.0704.001
viewGRangesWinSummary_dt2.7550.0633.555
within_clust_sort2.4700.0163.026