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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1919/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.27.2  (landing page)
Joseph R Boyd
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: ae10577
git_last_commit_date: 2024-12-09 15:04:05 -0500 (Mon, 09 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


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: 1.27.2
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_1.27.2.tar.gz
StartedAt: 2024-12-22 21:25:09 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 21:28:23 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 194.4 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_1.27.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.27.2’
* 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/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 
> ## 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 1291 ]
> 
> proc.time()
   user  system elapsed 
 74.979   1.545  76.754 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation0.9990.0201.038
append_ynorm0.0170.0020.018
applyMovingAverage0.2060.0050.220
applySpline0.1000.0030.104
assemble_heatmap_cluster_bars0.2120.0030.214
calc_norm_factors0.0100.0020.011
centerAtMax0.0830.0020.093
centerFixedSizeGRanges0.0450.0040.049
centerGRangesAtMax0.1520.0040.156
clusteringKmeans0.0110.0020.013
clusteringKmeansNestedHclust0.0120.0020.014
col2hex000
collapse_gr0.2120.0040.218
convert_collapsed_coord0.0610.0040.067
copy_clust_info0.4600.0050.464
crossCorrByRle0.1160.0030.119
easyLoad_FUN0.0150.0000.015
easyLoad_IDRmerged0.0110.0000.013
easyLoad_bed0.0350.0010.035
easyLoad_broadPeak0.0110.0000.011
easyLoad_narrowPeak0.0100.0010.010
easyLoad_seacr0.0100.0000.011
expandCigar0.0460.0040.050
findMaxPos0.0130.0030.016
fragLen_calcStranded0.4510.0120.470
fragLen_fromMacs2Xls0.0000.0010.001
getReadLength0.0170.0040.023
get_mapped_reads0.0030.0000.004
ggellipse0.1630.0020.165
harmonize_seqlengths0.0340.0030.037
make_clustering_matrix0.0260.0010.026
merge_clusters0.9430.0140.959
prepare_fetch_GRanges0.0080.0010.010
prepare_fetch_GRanges_names0.0220.0010.023
prepare_fetch_GRanges_width0.0080.0000.008
quantileGRangesWidth0.0060.0000.006
reorder_clusters_hclust0.5560.0050.562
reorder_clusters_manual0.2920.0050.296
reorder_clusters_stepdown0.5630.0050.573
reverse_clusters0.6510.0120.668
safeBrew0.0080.0010.010
split_cluster0.8760.0220.905
ssvAnnotateSubjectGRanges0.2730.0090.281
ssvConsensusIntervalSets0.1010.0040.106
ssvFactorizeMembTable0.0050.0010.006
ssvFeatureBars0.1490.0020.151
ssvFeatureBinaryHeatmap2.6610.2282.973
ssvFeatureEuler0.1600.0040.165
ssvFeaturePie0.1400.0150.155
ssvFeatureUpset0.7110.0150.726
ssvFeatureVenn0.2570.0040.260
ssvFetchBam1.5910.0981.690
ssvFetchBamPE0.5410.0570.600
ssvFetchBamPE.RNA0.4430.0230.470
ssvFetchBigwig0.4030.0100.413
ssvFetchGRanges0.2110.0010.212
ssvFetchSignal0.4130.0110.423
ssvMakeMembTable-methods0.1480.0040.174
ssvOverlapIntervalSets0.0720.0030.077
ssvSignalBandedQuantiles1.0390.0181.063
ssvSignalClustering0.7660.0170.783
ssvSignalHeatmap.ClusterBars0.9130.0100.935
ssvSignalHeatmap1.0890.0231.117
ssvSignalLineplot0.6150.0090.625
ssvSignalLineplotAgg0.2190.0020.222
ssvSignalScatterplot0.2950.0110.306
viewGRangesWinSample_dt0.3460.0080.362
viewGRangesWinSummary_dt0.3370.0100.348
within_clust_sort0.4290.0040.436