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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1897/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.25.2  (landing page)
Joseph R Boyd
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 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
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for seqsetvis on palomino6

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: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings seqsetvis_1.25.2.tar.gz
StartedAt: 2024-07-16 04:03:55 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 04:22:22 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 1107.4 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings seqsetvis_1.25.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.25.2'
* 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 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  9.20   0.47   14.86
ssvSignalBandedQuantiles 7.62   0.13    9.98
ssvSignalHeatmap         7.19   0.02    7.33
add_cluster_annotation   6.12   0.22    6.58
copy_clust_info          6.20   0.08    6.31
viewGRangesWinSample_dt  5.33   0.05    7.12
* 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:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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 
 293.04   13.10  308.73 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation6.120.226.58
append_ynorm0.050.030.08
applyMovingAverage0.530.060.61
applySpline0.250.050.31
assemble_heatmap_cluster_bars1.920.002.38
calc_norm_factors0.020.030.05
centerAtMax0.210.020.23
centerFixedSizeGRanges0.110.020.12
centerGRangesAtMax0.290.080.36
clusteringKmeans0.010.040.06
clusteringKmeansNestedHclust0.020.050.07
col2hex000
collapse_gr0.560.000.56
convert_collapsed_coord0.180.000.17
copy_clust_info6.200.086.31
crossCorrByRle0.270.000.27
easyLoad_FUN0.040.000.05
easyLoad_IDRmerged0.030.000.03
easyLoad_bed0.100.000.09
easyLoad_broadPeak0.030.000.03
easyLoad_narrowPeak0.030.000.03
easyLoad_seacr0.030.000.04
expandCigar0.130.020.14
findMaxPos0.030.030.07
fragLen_calcStranded3.170.053.46
fragLen_fromMacs2Xls000
getReadLength0.050.000.04
get_mapped_reads0.010.000.02
ggellipse0.440.000.44
harmonize_seqlengths0.080.010.09
make_clustering_matrix0.030.060.09
merge_clusters2.590.052.65
prepare_fetch_GRanges0.020.000.03
prepare_fetch_GRanges_names0.590.020.61
prepare_fetch_GRanges_width0.040.000.05
quantileGRangesWidth0.020.000.01
reorder_clusters_hclust2.580.063.21
reorder_clusters_manual1.650.032.15
reorder_clusters_stepdown1.410.111.52
reverse_clusters2.470.092.80
safeBrew0.010.000.01
split_cluster2.470.103.77
ssvAnnotateSubjectGRanges0.720.030.75
ssvConsensusIntervalSets0.250.000.25
ssvFactorizeMembTable0.010.000.01
ssvFeatureBars0.470.000.47
ssvFeatureBinaryHeatmap 9.20 0.4714.86
ssvFeatureEuler0.400.030.42
ssvFeaturePie0.390.000.39
ssvFeatureUpset3.280.073.34
ssvFeatureVenn0.720.030.75
ssvFetchBam000
ssvFetchBamPE000
ssvFetchBamPE.RNA1.100.081.25
ssvFetchBigwig000
ssvFetchGRanges0.570.010.60
ssvFetchSignal2.050.052.25
ssvMakeMembTable-methods0.450.000.45
ssvOverlapIntervalSets0.180.010.19
ssvSignalBandedQuantiles7.620.139.98
ssvSignalClustering3.840.063.99
ssvSignalHeatmap.ClusterBars3.830.063.84
ssvSignalHeatmap7.190.027.33
ssvSignalLineplot3.440.034.42
ssvSignalLineplotAgg0.640.000.66
ssvSignalScatterplot0.610.050.67
viewGRangesWinSample_dt5.330.057.12
viewGRangesWinSummary_dt0.890.000.93
within_clust_sort1.180.031.20