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This page was generated on 2024-05-04 11:39:58 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1948/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.24.0  (landing page)
Joseph R Boyd
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_19
git_last_commit: 17d8408
git_last_commit_date: 2024-04-30 11:05:16 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for seqsetvis on lconway


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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2024-05-04 00:53:49 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:05:10 -0400 (Sat, 04 May 2024)
EllapsedTime: 680.7 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.24.0’
* 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 8.647  0.765    9.51
ssvFetchBam             7.234  0.389    7.71
* 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-x86_64/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 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 
301.160   8.636 312.768 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.3480.0983.486
append_ynorm0.0440.0060.052
applyMovingAverage0.7740.0710.858
applySpline0.3490.0090.363
assemble_heatmap_cluster_bars0.8230.0140.844
calc_norm_factors0.0160.0010.017
centerAtMax0.3430.0110.357
centerFixedSizeGRanges0.1910.0140.208
centerGRangesAtMax0.4190.0060.427
clusteringKmeans0.0210.0020.022
clusteringKmeansNestedHclust0.0240.0030.027
col2hex0.0010.0000.001
collapse_gr0.9280.0230.960
convert_collapsed_coord0.2630.0160.280
copy_clust_info1.7960.0241.836
crossCorrByRle0.3870.0090.402
easyLoad_FUN0.0530.0020.056
easyLoad_IDRmerged0.0550.0020.058
easyLoad_bed0.1630.0020.168
easyLoad_broadPeak0.0450.0020.047
easyLoad_narrowPeak0.0410.0020.044
easyLoad_seacr0.0560.0020.061
expandCigar0.2000.0180.221
findMaxPos0.0160.0030.019
fragLen_calcStranded1.8550.0431.916
fragLen_fromMacs2Xls0.0030.0010.004
getReadLength0.0620.0060.068
get_mapped_reads0.0090.0010.009
ggellipse0.6230.0110.642
harmonize_seqlengths0.1450.0140.164
make_clustering_matrix0.0450.0020.047
merge_clusters3.8580.0663.972
prepare_fetch_GRanges0.0350.0010.036
prepare_fetch_GRanges_names0.0950.0020.097
prepare_fetch_GRanges_width0.0360.0020.038
quantileGRangesWidth0.0020.0000.002
reorder_clusters_hclust2.2510.0352.314
reorder_clusters_manual1.1060.0321.159
reorder_clusters_stepdown2.2160.0272.264
reverse_clusters2.3490.0332.402
safeBrew0.0270.0040.032
split_cluster2.0920.0532.168
ssvConsensusIntervalSets0.4030.0190.425
ssvFactorizeMembTable0.0150.0020.017
ssvFeatureBars0.6140.0160.638
ssvFeatureBinaryHeatmap8.6470.7659.510
ssvFeatureEuler0.5960.0140.617
ssvFeaturePie0.6430.0410.690
ssvFeatureUpset2.8560.0692.963
ssvFeatureVenn1.0640.0221.101
ssvFetchBam7.2340.3897.710
ssvFetchBamPE2.4360.2292.698
ssvFetchBigwig1.7300.0371.785
ssvFetchGRanges0.8960.0110.915
ssvFetchSignal1.7900.0741.884
ssvMakeMembTable-methods0.6400.0190.666
ssvOverlapIntervalSets0.3210.0150.339
ssvSignalBandedQuantiles4.1900.0824.312
ssvSignalClustering2.4620.0532.544
ssvSignalHeatmap.ClusterBars3.5870.1303.760
ssvSignalHeatmap4.0600.0944.210
ssvSignalLineplot2.5550.0332.620
ssvSignalLineplotAgg0.9170.0140.943
ssvSignalScatterplot1.0210.0151.044
viewGRangesWinSample_dt1.4530.0611.533
viewGRangesWinSummary_dt1.3960.0871.504
within_clust_sort1.6850.0401.751