Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-12-23 12:05 -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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings seqsetvis_1.26.0.tar.gz
StartedAt: 2024-12-20 05:56:26 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:07:30 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 664.0 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings seqsetvis_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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  7.8   0.47    8.34
* 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 37 | PASS 818 ]

══ Skipped tests (37) ══════════════════════════════════════════════════════════
• On Windows (37): 'test_anchor.R:203:5', 'test_anchor.R:258:5',
  'test_fetchBam.R:98:5', 'test_fetchBam.R:142:5', 'test_fetchBam.R:170:5',
  'test_fetchBam.R:201:5', 'test_fetchBw.R:17:5', 'test_fetchBw.R:32:5',
  'test_fetchBw.R:46:5', 'test_fetchBw.R:63:5', 'test_fetchBw.R:73:5',
  'test_fetchBw.R:86:5', 'test_fetchBw.R:97:5', 'test_fetchBw.R:108:5',
  'test_fetchBw.R:120:5', 'test_fetchBw.R:143:5', 'test_fetchBw.R:153:5',
  'test_fetchBw.R:165:5', 'test_fetchBw.R:175:5', 'test_fetchBw.R:190:5',
  'test_fetchBw.R:205:5', 'test_fetchBw.R:220:5', 'test_fetchBw_dt.R:15:5',
  'test_fetchBw_dt.R:31:5', 'test_fetchBw_dt.R:46:5', 'test_fetchBw_dt.R:64:5',
  'test_fetchBw_dt.R:74:5', 'test_fetchBw_dt.R:87:5', 'test_fetchBw_dt.R:98:5',
  'test_fetchBw_dt.R:109:5', 'test_fetchBw_dt.R:121:5',
  'test_fetchBw_dt.R:133:5', 'test_fetch_parallel.R:16:5',
  'test_fetch_parallel.R:44:5', 'test_force_skip.R:33:5',
  'test_viewGrangesWin_sample_vs_summary.R:115:5',
  'test_viewGrangesWin_sample_vs_summary.R:136:5'

[ FAIL 0 | WARN 0 | SKIP 37 | PASS 818 ]
> 
> proc.time()
   user  system elapsed 
 251.65    5.04  258.14 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.910.154.06
append_ynorm0.030.100.13
applyMovingAverage0.890.060.97
applySpline0.390.060.45
assemble_heatmap_cluster_bars0.860.060.92
calc_norm_factors0.030.100.13
centerAtMax0.300.010.31
centerFixedSizeGRanges0.160.000.16
centerGRangesAtMax0.500.080.58
clusteringKmeans0.030.080.11
clusteringKmeansNestedHclust0.030.060.09
col2hex000
collapse_gr0.830.030.86
convert_collapsed_coord0.250.050.30
copy_clust_info2.050.062.11
crossCorrByRle0.420.020.44
easyLoad_FUN0.080.000.07
easyLoad_IDRmerged0.080.000.08
easyLoad_bed0.150.010.17
easyLoad_broadPeak0.050.000.05
easyLoad_narrowPeak0.030.000.03
easyLoad_seacr0.040.000.04
expandCigar0.220.040.25
findMaxPos0.080.040.13
fragLen_calcStranded2.020.052.06
fragLen_fromMacs2Xls000
getReadLength0.070.020.10
get_mapped_reads0.020.000.01
ggellipse0.560.030.59
harmonize_seqlengths0.140.030.18
make_clustering_matrix0.140.030.17
merge_clusters3.910.114.05
prepare_fetch_GRanges0.010.010.03
prepare_fetch_GRanges_names0.080.000.08
prepare_fetch_GRanges_width0.030.000.03
quantileGRangesWidth0.020.000.01
reorder_clusters_hclust2.340.092.44
reorder_clusters_manual1.410.021.42
reorder_clusters_stepdown2.370.082.46
reverse_clusters2.670.082.78
safeBrew0.020.000.01
split_cluster3.250.233.49
ssvAnnotateSubjectGRanges1.260.051.31
ssvConsensusIntervalSets0.320.040.36
ssvFactorizeMembTable0.010.020.03
ssvFeatureBars0.750.010.77
ssvFeatureBinaryHeatmap7.800.478.34
ssvFeatureEuler0.730.000.73
ssvFeaturePie0.660.020.67
ssvFeatureUpset3.230.113.34
ssvFeatureVenn1.030.061.10
ssvFetchBam000
ssvFetchBamPE000
ssvFetchBamPE.RNA1.890.081.97
ssvFetchBigwig000
ssvFetchGRanges1.060.051.11
ssvFetchSignal1.940.062.00
ssvMakeMembTable-methods0.610.000.61
ssvOverlapIntervalSets0.390.000.39
ssvSignalBandedQuantiles4.750.224.98
ssvSignalClustering3.060.043.11
ssvSignalHeatmap.ClusterBars3.630.103.72
ssvSignalHeatmap4.620.084.70
ssvSignalLineplot2.610.062.67
ssvSignalLineplotAgg1.100.051.18
ssvSignalScatterplot1.170.011.20
viewGRangesWinSample_dt1.340.021.36
viewGRangesWinSummary_dt1.170.001.17
within_clust_sort1.580.101.67