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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1934/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.26.0  (landing page)
Joseph R Boyd
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_20
git_last_commit: 31e216f
git_last_commit_date: 2024-10-29 10:27:03 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for seqsetvis on kjohnson1

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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2024-12-21 09:10:47 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 09:21:14 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 626.8 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.26.0’
* 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 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 7.525  0.586   8.186
ssvFetchBam             6.964  0.284   6.197
ssvSignalHeatmap        5.519  0.296   3.934
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 
299.761   9.884 272.745 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.3760.0953.254
append_ynorm0.0940.0130.068
applyMovingAverage0.8960.0720.769
applySpline0.5830.0340.337
assemble_heatmap_cluster_bars0.9980.0430.725
calc_norm_factors0.0430.0040.036
centerAtMax0.5630.0380.326
centerFixedSizeGRanges0.3000.0230.173
centerGRangesAtMax0.6570.0470.398
clusteringKmeans0.0710.0090.041
clusteringKmeansNestedHclust0.0740.0090.044
col2hex0.0030.0010.002
collapse_gr0.8270.0270.794
convert_collapsed_coord0.2290.0090.239
copy_clust_info2.6600.1261.674
crossCorrByRle0.3310.0070.339
easyLoad_FUN0.0530.0020.055
easyLoad_IDRmerged0.0450.0020.051
easyLoad_bed0.1200.0010.122
easyLoad_broadPeak0.0350.0010.037
easyLoad_narrowPeak0.0390.0010.040
easyLoad_seacr0.0430.0020.046
expandCigar0.2130.0140.183
findMaxPos0.0910.0140.056
fragLen_calcStranded1.8240.0591.634
fragLen_fromMacs2Xls0.0060.0010.004
getReadLength0.0680.0050.080
get_mapped_reads0.0090.0010.011
ggellipse0.5200.0060.544
harmonize_seqlengths0.1230.0100.133
make_clustering_matrix0.1350.0090.087
merge_clusters3.8750.1183.223
prepare_fetch_GRanges0.0280.0030.030
prepare_fetch_GRanges_names0.0780.0040.082
prepare_fetch_GRanges_width0.0190.0010.021
quantileGRangesWidth0.0030.0020.004
reorder_clusters_hclust1.7440.0421.795
reorder_clusters_manual1.2400.0441.026
reorder_clusters_stepdown2.1250.0531.818
reverse_clusters3.5240.0863.133
safeBrew0.0270.0030.031
split_cluster2.1920.0771.786
ssvAnnotateSubjectGRanges0.9560.0200.979
ssvConsensusIntervalSets0.3580.0090.371
ssvFactorizeMembTable0.0160.0030.019
ssvFeatureBars0.5250.0060.537
ssvFeatureBinaryHeatmap7.5250.5868.186
ssvFeatureEuler0.5310.0150.549
ssvFeaturePie0.4850.0120.504
ssvFeatureUpset2.4530.0242.492
ssvFeatureVenn0.8890.0120.906
ssvFetchBam6.9640.2846.197
ssvFetchBamPE2.0140.1142.141
ssvFetchBamPE.RNA2.0050.0941.552
ssvFetchBigwig1.6500.0591.539
ssvFetchGRanges0.7560.0130.770
ssvFetchSignal1.5650.0571.628
ssvMakeMembTable-methods0.5600.0140.577
ssvOverlapIntervalSets0.2690.0090.277
ssvSignalBandedQuantiles4.7660.1973.601
ssvSignalClustering3.8970.1812.697
ssvSignalHeatmap.ClusterBars4.3960.1723.213
ssvSignalHeatmap5.5190.2963.934
ssvSignalLineplot2.3390.0402.215
ssvSignalLineplotAgg1.1930.0620.783
ssvSignalScatterplot1.5010.0840.889
viewGRangesWinSample_dt1.3810.0551.259
viewGRangesWinSummary_dt1.4710.0721.181
within_clust_sort1.8470.0621.465