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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2121/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.36.2  (landing page)
Jianhong Ou
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/trackViewer
git_branch: RELEASE_3_17
git_last_commit: 8660ccc
git_last_commit_date: 2023-05-17 09:52:56 -0400 (Wed, 17 May 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for trackViewer on kjohnson2


To the developers/maintainers of the trackViewer package:
- 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: trackViewer
Version: 1.36.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings trackViewer_1.36.2.tar.gz
StartedAt: 2023-10-19 07:38:52 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 07:54:30 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 938.7 seconds
RetCode: 0
Status:   OK  
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings trackViewer_1.36.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/trackViewer.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.36.2’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
trackViewer-package 28.663  0.371  51.997
parseWIG            19.811  0.234  35.477
viewTracks          19.404  0.371  35.443
browseTracks        18.328  0.185  32.259
geneModelFromTxdb    7.474  0.298  13.826
viewGene             7.328  0.244  13.454
GRoperator           4.085  0.169   6.839
dandelion.plot       3.004  0.034   5.449
importData           2.847  0.041   5.128
geneTrack            2.763  0.063   5.034
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

trackViewer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL trackViewer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> 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, setdiff, sort, 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 -- Thu Oct 19 07:54:11 2023 
*********************************************** 
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 
 19.733   1.075  35.488 

Example timings

trackViewer.Rcheck/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator4.0850.1696.839
addArrowMark0.0090.0010.016
addGuideLine0.0050.0000.011
browseTracks18.328 0.18532.259
coverageGR0.2800.0040.516
dandelion.plot3.0040.0345.449
geneModelFromTxdb 7.474 0.29813.826
geneTrack2.7630.0635.034
getCurTrackViewport0.0030.0010.007
getGeneIDsFromTxDb1.1570.0332.064
getLocation1.8810.1133.505
gi2track0.0590.0030.117
gieStain0.0060.0010.015
ideogramPlot000
importBam0.4110.0110.760
importData2.8470.0415.128
importGInteractions0.7710.0261.439
importScSeqScore0.0000.0000.005
importScore0.8240.0211.504
listChromosomes0.5830.0131.071
listResolutions0.0040.0020.010
loadIdeogram000
lolliplot1.2790.0172.297
optimizeStyle0.6990.0141.271
parse2GRanges0.0130.0010.022
parseWIG19.811 0.23435.477
plotGInteractions1.6420.0682.649
plotGRanges2.0910.0453.373
plotIdeo000
plotOneIdeo000
trackStyle-class0.0580.0020.106
trackViewer-package28.663 0.37151.997
trackViewerStyle-class0.0000.0000.001
viewGene 7.328 0.24413.454
viewTracks19.404 0.37135.443