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This page was generated on 2024-03-27 11:38:41 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 1919/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.23.9  (landing page)
Joseph R Boyd
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/seqsetvis
git_branch: devel
git_last_commit: 8703651
git_last_commit_date: 2024-03-15 16:24:53 -0400 (Fri, 15 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for seqsetvis on palomino3


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: 1.23.9
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings seqsetvis_1.23.9.tar.gz
StartedAt: 2024-03-27 06:24:39 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 06:34:53 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 613.2 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings seqsetvis_1.23.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/seqsetvis.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 '1.23.9'
* 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 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 8.93   0.49    9.45
* 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-3.19-bioc\R\bin\R.exe CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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 800 ]

══ 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 800 ]
> 
> proc.time()
   user  system elapsed 
 225.21    5.71  231.28 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.060.053.11
append_ynorm0.040.000.05
applyMovingAverage0.710.060.76
applySpline0.290.020.32
assemble_heatmap_cluster_bars0.770.000.76
calc_norm_factors0.020.000.02
centerAtMax0.260.000.26
centerFixedSizeGRanges0.170.000.18
centerGRangesAtMax0.390.000.39
clusteringKmeans0.020.000.01
clusteringKmeansNestedHclust0.030.000.03
col2hex000
collapse_gr0.860.030.89
convert_collapsed_coord0.180.030.22
copy_clust_info1.690.031.73
crossCorrByRle0.340.000.36
easyLoad_FUN0.040.000.04
easyLoad_IDRmerged0.070.000.08
easyLoad_bed0.110.000.11
easyLoad_broadPeak0.030.000.05
easyLoad_narrowPeak0.040.000.05
easyLoad_seacr0.030.000.04
expandCigar0.180.000.19
findMaxPos0.020.000.02
fragLen_calcStranded1.550.091.65
fragLen_fromMacs2Xls0.010.000.02
getReadLength0.050.000.05
get_mapped_reads000
ggellipse0.570.000.58
harmonize_seqlengths0.110.020.12
make_clustering_matrix0.050.000.05
merge_clusters3.410.043.44
prepare_fetch_GRanges0.030.000.03
prepare_fetch_GRanges_names0.080.000.08
prepare_fetch_GRanges_width0.030.000.03
quantileGRangesWidth000
reorder_clusters_hclust2.090.022.11
reorder_clusters_manual1.080.031.12
reorder_clusters_stepdown2.050.022.07
reverse_clusters2.530.012.54
safeBrew0.030.000.03
split_cluster2.010.072.08
ssvConsensusIntervalSets0.410.010.42
ssvFactorizeMembTable0.010.000.01
ssvFeatureBars0.560.000.57
ssvFeatureBinaryHeatmap8.930.499.45
ssvFeatureEuler0.560.040.61
ssvFeaturePie0.440.050.48
ssvFeatureUpset2.890.052.94
ssvFeatureVenn1.140.031.17
ssvFetchBam000
ssvFetchBamPE000
ssvFetchBigwig000
ssvFetchGRanges0.890.010.91
ssvFetchSignal1.900.021.92
ssvMakeMembTable-methods0.660.000.66
ssvOverlapIntervalSets0.230.010.25
ssvSignalBandedQuantiles4.140.134.32
ssvSignalClustering2.330.082.43
ssvSignalHeatmap.ClusterBars3.840.103.97
ssvSignalHeatmap3.890.073.98
ssvSignalLineplot2.990.043.02
ssvSignalLineplotAgg0.830.010.84
ssvSignalScatterplot0.790.000.80
viewGRangesWinSample_dt1.470.061.53
viewGRangesWinSummary_dt1.270.051.30
within_clust_sort1.820.021.84