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CHECK report for Gviz on merida1

This page was generated on 2019-04-16 11:56:14 -0400 (Tue, 16 Apr 2019).

Package 701/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.26.5
Robert Ivanek
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Gviz
Branch: RELEASE_3_8
Last Commit: 430310b
Last Changed Date: 2019-02-21 05:21:43 -0400 (Thu, 21 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Gviz
Version: 1.26.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Gviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Gviz_1.26.5.tar.gz
StartedAt: 2019-04-16 00:29:29 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:36:44 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 434.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Gviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Gviz_1.26.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Gviz.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.26.5’
* 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 ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   2.1Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AlignmentsTrack-class 13.791  1.242  15.210
SequenceTrack-class    9.802  0.809  10.738
AnnotationTrack-class  7.790  0.170   8.046
GeneRegionTrack-class  6.919  0.050   7.041
plotTracks             6.554  0.124   6.828
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Gviz.Rcheck/00check.log’
for details.



Installation output

Gviz.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Gviz
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Gviz’ ...
** 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
* DONE (Gviz)

Tests output


Example timings

Gviz.Rcheck/Gviz-Ex.timings

nameusersystemelapsed
AlignedReadTrack-class4.0830.1114.244
AlignmentsTrack-class13.791 1.24215.210
AnnotationTrack-class7.7900.1708.046
BiomartGeneRegionTrack-class4.3440.0404.413
DataTrack-class0.8910.0150.910
DisplayPars-class0.0250.0020.027
GeneRegionTrack-class6.9190.0507.041
GenomeAxisTrack-class4.2810.0134.339
IdeogramTrack-class1.2500.0201.276
SequenceTrack-class 9.802 0.80910.738
plotTracks6.5540.1246.828