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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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 teran2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqsetvis_1.26.0.tar.gz
StartedAt: 2024-11-20 09:36:51 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 09:46:17 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 565.8 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqsetvis_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 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 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 5.582  0.233   6.533
ssvFetchBam             4.818  0.008   5.158
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

seqsetvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 1284 ]
> 
> proc.time()
   user  system elapsed 
203.199   2.203 223.629 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation3.0370.1104.227
append_ynorm0.0520.0030.039
applyMovingAverage0.4740.0000.470
applySpline0.2690.0000.240
assemble_heatmap_cluster_bars0.5400.0010.562
calc_norm_factors0.0290.0000.021
centerAtMax0.2380.0010.190
centerFixedSizeGRanges0.0780.0010.080
centerGRangesAtMax0.3110.0070.320
clusteringKmeans0.0350.0040.039
clusteringKmeansNestedHclust0.0330.0010.024
col2hex0.0000.0010.001
collapse_gr0.4380.0010.446
convert_collapsed_coord0.1180.0010.120
copy_clust_info1.2130.0051.288
crossCorrByRle0.2170.0010.224
easyLoad_FUN0.0350.0010.038
easyLoad_IDRmerged0.0440.0000.045
easyLoad_bed0.0860.0000.085
easyLoad_broadPeak0.0250.0000.027
easyLoad_narrowPeak0.0270.0000.050
easyLoad_seacr0.0300.0000.035
expandCigar0.1260.0020.112
findMaxPos0.0350.0000.047
fragLen_calcStranded2.0440.0062.343
fragLen_fromMacs2Xls0.0020.0000.002
getReadLength0.0360.0010.040
get_mapped_reads0.0050.0010.006
ggellipse0.350.000.35
harmonize_seqlengths0.0530.0030.057
make_clustering_matrix0.0760.0040.085
merge_clusters2.7520.0143.181
prepare_fetch_GRanges0.0200.0020.022
prepare_fetch_GRanges_names0.0520.0020.053
prepare_fetch_GRanges_width0.0180.0020.019
quantileGRangesWidth0.0010.0010.002
reorder_clusters_hclust1.3580.0031.326
reorder_clusters_manual0.7570.0060.774
reorder_clusters_stepdown1.3650.0011.449
reverse_clusters1.6070.0171.755
safeBrew0.0170.0010.036
split_cluster2.6690.1333.384
ssvAnnotateSubjectGRanges0.6110.0060.724
ssvConsensusIntervalSets0.1950.0030.204
ssvFactorizeMembTable0.0090.0000.009
ssvFeatureBars0.3550.0010.459
ssvFeatureBinaryHeatmap5.5820.2336.533
ssvFeatureEuler0.3700.0020.374
ssvFeaturePie0.3360.0010.346
ssvFeatureUpset1.7060.0011.725
ssvFeatureVenn1.4070.0011.415
ssvFetchBam4.8180.0085.158
ssvFetchBamPE1.2890.0071.534
ssvFetchBamPE.RNA1.6900.0211.893
ssvFetchBigwig0.9380.0030.954
ssvFetchGRanges0.4910.0010.493
ssvFetchSignal1.4330.0021.531
ssvMakeMembTable-methods0.3170.0030.325
ssvOverlapIntervalSets0.1420.0020.144
ssvSignalBandedQuantiles2.6620.0042.590
ssvSignalClustering1.9920.0042.063
ssvSignalHeatmap.ClusterBars2.9270.0022.983
ssvSignalHeatmap2.7880.0192.657
ssvSignalLineplot1.4570.0011.561
ssvSignalLineplotAgg0.5510.0010.528
ssvSignalScatterplot0.6950.0030.800
viewGRangesWinSample_dt1.2000.0001.569
viewGRangesWinSummary_dt0.8440.0000.824
within_clust_sort1.1260.0021.198