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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).

CHECK results for Gviz on nebbiolo1

To the developers/maintainers of the Gviz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Gviz.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 831/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.36.2  (landing page)
Robert Ivanek
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Gviz
git_branch: RELEASE_3_13
git_last_commit: 742ed80
git_last_commit_date: 2021-07-02 05:34:16 -0400 (Fri, 02 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Gviz
Version: 1.36.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Gviz.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Gviz_1.36.2.tar.gz
StartedAt: 2021-10-14 10:07:46 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:16:03 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 496.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Gviz.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Gviz_1.36.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Gviz.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ 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 ‘Gviz’ 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 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
AlignmentsTrack-class 14.911  1.076  15.990
AnnotationTrack-class  8.217  0.160   8.377
GeneRegionTrack-class  6.997  0.108   7.105
plotTracks             6.223  0.068   6.355
GenomeAxisTrack-class  5.233  0.144   5.411
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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

Gviz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Gviz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘Gviz’ ...
** 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 (Gviz)

Tests output

Gviz.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> library(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("Gviz")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    pattern

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

    strsplit

Loading required package: rtracklayer
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 299 ]
> 
> proc.time()
   user  system elapsed 
 58.956  10.398  76.073 

Example timings

Gviz.Rcheck/Gviz-Ex.timings

nameusersystemelapsed
AlignmentsTrack-class14.911 1.07615.990
AnnotationTrack-class8.2170.1608.377
BiomartGeneRegionTrack-class3.5760.0553.630
CustomTrack-class0.0050.0010.006
DataTrack-class2.0890.0562.145
DisplayPars-class0.0180.0040.021
GdObject-class0.5200.0000.519
GeneRegionTrack-class6.9970.1087.105
GenomeAxisTrack-class5.2330.1445.411
HighlightTrack-class0.2110.0030.213
IdeogramTrack-class1.8130.5802.496
OverlayTrack-class0.0570.0000.057
RangeTrack-class0.5860.0000.585
ReferenceTrack-class2.7720.7163.488
SequenceTrack-class3.8541.0484.907
StackedTrack-class1.0670.1921.259
UcscTrack0.9340.0721.006
exportTracks0.1280.0000.128
plotTracks6.2230.0686.355
settings0.9350.0000.935