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This page was generated on 2024-11-20 12:08 -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 2174/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.42.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/trackViewer
git_branch: RELEASE_3_20
git_last_commit: 0438f5e
git_last_commit_date: 2024-10-29 09:49:56 -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 trackViewer on kunpeng2

To the developers/maintainers of the trackViewer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trackViewer.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: trackViewer
Version: 1.42.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings trackViewer_1.42.0.tar.gz
StartedAt: 2024-11-20 13:22:30 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 13:33:22 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 652.1 seconds
RetCode: 0
Status:   OK  
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings trackViewer_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/trackViewer.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.42.0’
* 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 ‘trackViewer’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
trackViewer-package 31.199  0.184  31.489
browseTracks        23.032  0.192  23.278
parseWIG            22.924  0.172  23.142
viewTracks          22.936  0.108  23.089
viewGene             7.228  0.059   7.302
geneModelFromTxdb    6.273  0.180   6.462
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

trackViewer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL trackViewer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘trackViewer’ ...
** using staged installation
** R
** 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 (trackViewer)

Tests output

trackViewer.Rcheck/tests/runTests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> require("trackViewer") || stop("unable to load Package:trackViewer")
Loading required package: trackViewer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: grid
[1] TRUE
> require("RUnit") || stop("unable to load Package:RUnit")
Loading required package: RUnit
[1] TRUE
> BiocGenerics:::testPackage("trackViewer")


RUNIT TEST PROTOCOL -- Wed Nov 20 13:33:18 2024 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trackViewer RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 22.827   0.938  23.721 

Example timings

trackViewer.Rcheck/trackViewer-Ex.timings

nameusersystemelapsed
ARA1.9870.1192.118
GIoperator0.6200.0120.633
GRoperator4.4820.0364.528
addArrowMark0.0120.0040.017
addGuideLine0.0050.0000.004
addInteractionAnnotation0.3940.0000.395
browseTracks23.032 0.19223.278
coverageGR0.3280.0040.332
dandelion.plot3.3560.0083.371
geneModelFromTxdb6.2730.1806.462
geneTrack2.8590.0162.880
getCurTrackViewport0.0040.0000.004
getGeneIDsFromTxDb1.1980.0041.205
getLocation2.0190.0232.047
gi2track0.070.000.07
gieStain0.0070.0000.007
ideogramPlot000
importBam0.4570.0000.458
importData3.8570.0363.900
importGInteractions0.4630.0120.483
importScSeqScore0.0000.0000.001
importScore0.8940.0000.897
listChromosomes0.0160.0000.016
listNormalizations0.0190.0000.020
listResolutions0.0060.0000.006
loadIdeogram000
lolliplot1.4730.0961.572
optimizeStyle0.7990.0110.813
parse2GRanges0.0170.0000.017
parseWIG22.924 0.17223.142
plotGRanges2.2860.0002.291
plotIdeo000
plotOneIdeo000
reduce-GInteractions-method000
trackStyle-class0.0690.0000.070
trackViewer-package31.199 0.18431.489
trackViewerStyle-class0.0000.0000.001
viewGene7.2280.0597.302
viewTracks22.936 0.10823.089