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This page was generated on 2024-07-24 11:42 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1902/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.25.2  (landing page)
Joseph R Boyd
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 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
palomino8Windows 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
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: 2024-07-24 00:53:11 -0400 (Wed, 24 Jul 2024)
EndedAt: 2024-07-24 00:56:17 -0400 (Wed, 24 Jul 2024)
EllapsedTime: 186.1 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 (2024-06-14)
* 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 13.6.7
* 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 (2024-06-14) -- "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 
 72.412   1.482  73.941 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation1.0060.0331.040
append_ynorm0.0170.0020.018
applyMovingAverage0.2010.0020.203
applySpline0.0970.0020.100
assemble_heatmap_cluster_bars0.2050.0010.207
calc_norm_factors0.0100.0010.010
centerAtMax0.0800.0020.083
centerFixedSizeGRanges0.0440.0030.047
centerGRangesAtMax0.1130.0040.116
clusteringKmeans0.0100.0010.012
clusteringKmeansNestedHclust0.0120.0010.013
col2hex0.0010.0000.001
collapse_gr0.1980.0030.203
convert_collapsed_coord0.0540.0020.056
copy_clust_info0.4630.0050.466
crossCorrByRle0.1020.0020.105
easyLoad_FUN0.0160.0010.017
easyLoad_IDRmerged0.0120.0000.013
easyLoad_bed0.0370.0010.037
easyLoad_broadPeak0.0100.0000.011
easyLoad_narrowPeak0.0110.0000.011
easyLoad_seacr0.0110.0010.012
expandCigar0.0480.0030.052
findMaxPos0.0130.0030.016
fragLen_calcStranded0.4410.0060.448
fragLen_fromMacs2Xls0.0010.0010.001
getReadLength0.0170.0010.018
get_mapped_reads0.0030.0000.003
ggellipse0.1610.0010.163
harmonize_seqlengths0.0330.0030.036
make_clustering_matrix0.0200.0010.022
merge_clusters0.9480.0080.960
prepare_fetch_GRanges0.0080.0010.009
prepare_fetch_GRanges_names0.0220.0010.023
prepare_fetch_GRanges_width0.0080.0010.010
quantileGRangesWidth0.0010.0000.001
reorder_clusters_hclust0.5260.0050.530
reorder_clusters_manual0.2810.0030.285
reorder_clusters_stepdown0.5640.0130.578
reverse_clusters0.5820.0110.593
safeBrew0.0100.0010.011
split_cluster0.4910.0060.497
ssvAnnotateSubjectGRanges0.5760.0100.586
ssvConsensusIntervalSets0.0890.0030.098
ssvFactorizeMembTable0.0050.0010.005
ssvFeatureBars0.1570.0020.159
ssvFeatureBinaryHeatmap2.3790.1902.571
ssvFeatureEuler0.1390.0030.142
ssvFeaturePie0.1250.0100.135
ssvFeatureUpset0.6560.0100.666
ssvFeatureVenn0.2350.0020.238
ssvFetchBam1.5840.0451.629
ssvFetchBamPE0.5360.0290.566
ssvFetchBamPE.RNA0.3980.0120.410
ssvFetchBigwig0.3850.0070.393
ssvFetchGRanges0.2030.0010.205
ssvFetchSignal0.4020.0120.417
ssvMakeMembTable-methods0.1470.0030.149
ssvOverlapIntervalSets0.0680.0030.071
ssvSignalBandedQuantiles1.0500.0161.073
ssvSignalClustering0.7310.0110.742
ssvSignalHeatmap.ClusterBars0.9070.0210.927
ssvSignalHeatmap1.0100.0191.029
ssvSignalLineplot0.6090.0030.613
ssvSignalLineplotAgg0.2140.0030.216
ssvSignalScatterplot0.2460.0050.251
viewGRangesWinSample_dt0.3250.0130.339
viewGRangesWinSummary_dt0.3170.0070.325
within_clust_sort0.3980.0040.403