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This page was generated on 2024-03-27 11:37:11 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1930/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.22.1  (landing page)
Joseph R Boyd
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: RELEASE_3_18
git_last_commit: 6084d0e
git_last_commit_date: 2024-03-07 18:16:11 -0400 (Thu, 07 Mar 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for seqsetvis on palomino4


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: 1.22.1
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings seqsetvis_1.22.1.tar.gz
StartedAt: 2024-03-26 05:09:50 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 05:19:29 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 578.8 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings seqsetvis_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/seqsetvis.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* 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 '1.22.1'
* 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 R 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
ssvFeatureBinaryHeatmap 8.06   0.25    8.37
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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-3.18-bioc\R\bin\R.exe CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 787 ]

══ Skipped tests (37) ══════════════════════════════════════════════════════════
• On Windows (37): 'test_anchor.R:108:5', 'test_anchor.R:163:5',
  '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 787 ]
> 
> proc.time()
   user  system elapsed 
 202.51    4.40  208.90 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation2.470.112.60
append_ynorm0.010.000.03
applyMovingAverage2.100.002.09
applySpline0.340.020.34
assemble_heatmap_cluster_bars0.700.000.71
calc_norm_factors0.020.000.01
centerAtMax0.230.000.24
centerFixedSizeGRanges0.110.030.14
centerGRangesAtMax0.350.040.39
clusteringKmeans0.010.000.01
clusteringKmeansNestedHclust0.020.020.03
col2hex000
collapse_gr0.970.020.99
convert_collapsed_coord0.220.010.23
copy_clust_info1.930.021.97
crossCorrByRle0.470.030.53
easyLoad_FUN0.110.010.13
easyLoad_IDRmerged0.050.000.06
easyLoad_bed0.110.020.13
easyLoad_broadPeak0.060.000.06
easyLoad_narrowPeak0.060.000.06
easyLoad_seacr0.070.000.06
expandCigar0.170.000.17
findMaxPos0.010.000.02
fragLen_calcStranded1.530.021.55
fragLen_fromMacs2Xls0.000.000.01
getReadLength0.050.000.05
get_mapped_reads0.000.010.02
ggellipse0.50.00.5
harmonize_seqlengths0.110.000.10
make_clustering_matrix0.050.000.05
merge_clusters3.060.053.13
prepare_fetch_GRanges0.020.000.01
prepare_fetch_GRanges_names0.060.000.06
prepare_fetch_GRanges_width0.030.000.03
quantileGRangesWidth000
reorder_clusters_hclust2.360.002.36
reorder_clusters_manual0.870.030.91
reorder_clusters_stepdown1.740.001.73
reverse_clusters2.010.002.03
safeBrew0.010.000.01
split_cluster1.680.071.75
ssvConsensusIntervalSets0.310.060.38
ssvFactorizeMembTable0.010.000.01
ssvFeatureBars0.570.000.57
ssvFeatureBinaryHeatmap8.060.258.37
ssvFeatureEuler0.470.000.47
ssvFeaturePie0.490.060.54
ssvFeatureUpset2.900.032.96
ssvFeatureVenn1.080.021.09
ssvFetchBam000
ssvFetchBamPE000
ssvFetchBigwig000
ssvFetchGRanges0.770.010.78
ssvFetchSignal2.150.052.20
ssvMakeMembTable-methods0.520.020.54
ssvOverlapIntervalSets0.220.010.23
ssvSignalBandedQuantiles4.010.034.04
ssvSignalClustering2.220.032.27
ssvSignalHeatmap.ClusterBars2.850.132.98
ssvSignalHeatmap3.860.124.22
ssvSignalLineplot2.480.032.52
ssvSignalLineplotAgg0.810.020.83
ssvSignalScatterplot0.960.010.96
viewGRangesWinSample_dt1.060.031.10
viewGRangesWinSummary_dt0.950.040.98
within_clust_sort1.50.01.5