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This page was generated on 2024-05-07 11:32:45 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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Package 1948/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.24.0  (landing page)
Joseph R Boyd
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 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)
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:
- 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: 2024-05-07 00:54:11 -0400 (Tue, 07 May 2024)
EndedAt: 2024-05-07 00:57:06 -0400 (Tue, 07 May 2024)
EllapsedTime: 175.0 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/seqsetvis.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* 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
* 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
*** 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 (2024-04-24) -- "Puppy Cup"
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 1266 ]
> 
> proc.time()
   user  system elapsed 
 66.486   1.337  67.844 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation0.9390.0180.958
append_ynorm0.0110.0020.013
applyMovingAverage0.2000.0150.216
applySpline0.0890.0020.091
assemble_heatmap_cluster_bars0.1960.0020.198
calc_norm_factors0.0040.0000.004
centerAtMax0.0810.0020.084
centerFixedSizeGRanges0.0420.0030.045
centerGRangesAtMax0.0980.0010.099
clusteringKmeans0.0050.0000.005
clusteringKmeansNestedHclust0.0060.0010.007
col2hex000
collapse_gr0.1910.0040.194
convert_collapsed_coord0.0530.0030.056
copy_clust_info0.4380.0060.444
crossCorrByRle0.0930.0020.095
easyLoad_FUN0.0170.0010.017
easyLoad_IDRmerged0.0140.0010.014
easyLoad_bed0.0370.0000.038
easyLoad_broadPeak0.0110.0000.011
easyLoad_narrowPeak0.0100.0010.011
easyLoad_seacr0.0120.0000.012
expandCigar0.0440.0030.047
findMaxPos0.0040.0010.005
fragLen_calcStranded0.4350.0070.442
fragLen_fromMacs2Xls0.0000.0010.002
getReadLength0.0130.0010.014
get_mapped_reads0.0020.0000.002
ggellipse0.1270.0020.129
harmonize_seqlengths0.0250.0020.028
make_clustering_matrix0.0110.0010.011
merge_clusters0.7790.0090.788
prepare_fetch_GRanges0.0070.0000.006
prepare_fetch_GRanges_names0.0170.0000.017
prepare_fetch_GRanges_width0.0060.0000.006
quantileGRangesWidth0.0010.0000.000
reorder_clusters_hclust0.4730.0030.477
reorder_clusters_manual0.2440.0020.247
reorder_clusters_stepdown0.4710.0040.475
reverse_clusters0.5060.0050.510
safeBrew0.0080.0010.008
split_cluster0.4620.0120.473
ssvConsensusIntervalSets0.0770.0070.085
ssvFactorizeMembTable0.0040.0010.004
ssvFeatureBars0.1400.0090.150
ssvFeatureBinaryHeatmap3.0410.1413.183
ssvFeatureEuler0.1460.0020.148
ssvFeaturePie0.1710.0090.181
ssvFeatureUpset0.6460.0070.654
ssvFeatureVenn0.2430.0030.245
ssvFetchBam1.5980.0541.652
ssvFetchBamPE0.5450.0150.561
ssvFetchBigwig0.3700.0060.376
ssvFetchGRanges0.1980.0010.199
ssvFetchSignal0.4040.0170.421
ssvMakeMembTable-methods0.1340.0030.137
ssvOverlapIntervalSets0.0670.0030.070
ssvSignalBandedQuantiles0.9650.0200.984
ssvSignalClustering0.5320.0080.540
ssvSignalHeatmap.ClusterBars0.8220.0190.841
ssvSignalHeatmap0.8980.0080.906
ssvSignalLineplot0.5890.0040.596
ssvSignalLineplotAgg0.1950.0070.203
ssvSignalScatterplot0.2330.0060.240
viewGRangesWinSample_dt0.3300.0110.340
viewGRangesWinSummary_dt0.3110.0060.318
within_clust_sort0.3950.0050.400