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This page was generated on 2024-05-04 11:41:06 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1948/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.24.0  (landing page)
Joseph R Boyd
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 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)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for seqsetvis on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: seqsetvis
Version: 1.24.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings seqsetvis_1.24.0.tar.gz
StartedAt: 2024-05-04 11:56:51 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:09:29 -0000 (Sat, 04 May 2024)
EllapsedTime: 758.4 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings seqsetvis_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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  9.458  0.172   9.646
ssvFetchBam              8.818  0.047   8.884
ssvSignalBandedQuantiles 5.160  0.020   5.178
* 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:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
349.376   2.471 352.198 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.9530.0884.043
append_ynorm0.0510.0000.048
applyMovingAverage0.9970.0041.002
applySpline0.4940.0000.495
assemble_heatmap_cluster_bars1.0440.0081.051
calc_norm_factors0.0150.0030.018
centerAtMax0.3790.0010.375
centerFixedSizeGRanges0.1950.0000.196
centerGRangesAtMax0.5080.0200.523
clusteringKmeans0.0260.0000.022
clusteringKmeansNestedHclust0.0330.0000.031
col2hex0.0020.0000.001
collapse_gr1.0030.0001.005
convert_collapsed_coord0.2630.0080.271
copy_clust_info2.2940.0242.316
crossCorrByRle0.4740.0120.489
easyLoad_FUN0.0680.0040.073
easyLoad_IDRmerged0.0590.0000.061
easyLoad_bed0.1800.0000.181
easyLoad_broadPeak0.0510.0000.053
easyLoad_narrowPeak0.0540.0000.055
easyLoad_seacr0.0590.0000.060
expandCigar0.2180.0040.221
findMaxPos0.0210.0000.020
fragLen_calcStranded2.5350.0242.563
fragLen_fromMacs2Xls0.0030.0000.004
getReadLength0.0730.0000.073
get_mapped_reads0.0110.0000.011
ggellipse0.7890.0040.794
harmonize_seqlengths0.1470.0000.147
make_clustering_matrix0.0630.0000.059
merge_clusters4.8600.0354.893
prepare_fetch_GRanges0.0410.0000.041
prepare_fetch_GRanges_names0.1160.0000.116
prepare_fetch_GRanges_width0.0410.0000.041
quantileGRangesWidth0.0020.0010.002
reorder_clusters_hclust2.8530.0202.871
reorder_clusters_manual1.4170.0041.417
reorder_clusters_stepdown2.8440.0322.875
reverse_clusters3.0650.0403.095
safeBrew0.0290.0040.032
split_cluster2.6720.0112.670
ssvConsensusIntervalSets0.4020.0160.419
ssvFactorizeMembTable0.0170.0000.017
ssvFeatureBars0.7300.0200.752
ssvFeatureBinaryHeatmap9.4580.1729.646
ssvFeatureEuler0.6780.0120.692
ssvFeaturePie1.7070.0361.746
ssvFeatureUpset3.2770.0563.340
ssvFeatureVenn1.2050.0001.207
ssvFetchBam8.8180.0478.884
ssvFetchBamPE2.6920.0002.701
ssvFetchBigwig1.8690.0321.911
ssvFetchGRanges0.9910.0000.993
ssvFetchSignal2.0930.0042.101
ssvMakeMembTable-methods0.6860.0080.695
ssvOverlapIntervalSets0.3180.0000.319
ssvSignalBandedQuantiles5.1600.0205.178
ssvSignalClustering2.7980.0392.832
ssvSignalHeatmap.ClusterBars4.2000.0004.181
ssvSignalHeatmap4.8760.0244.872
ssvSignalLineplot3.0160.0113.034
ssvSignalLineplotAgg1.0600.0081.071
ssvSignalScatterplot1.1330.0001.133
viewGRangesWinSample_dt1.7350.0041.742
viewGRangesWinSummary_dt1.6460.0081.656
within_clust_sort2.0650.0082.068