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CHECK report for Gviz on merida2

This page was generated on 2018-10-17 08:50:16 -0400 (Wed, 17 Oct 2018).

Package 667/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.24.0
Robert Ivanek
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Gviz
Branch: RELEASE_3_7
Last Commit: 3ee1eec
Last Changed Date: 2018-04-30 10:35:23 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Gviz
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2018-10-16 21:56:02 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:02:19 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 377.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

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### Running 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Gviz.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.24.0’
* 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         1.6Mb
    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 11.741  1.070  12.877
SequenceTrack-class    9.475  0.757  10.365
GeneRegionTrack-class  6.248  0.046   6.357
AnnotationTrack-class  5.871  0.120   6.019
plotTracks             5.526  0.080   5.656
* 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-3.7-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-class3.6840.0903.791
AlignmentsTrack-class11.741 1.07012.877
AnnotationTrack-class5.8710.1206.019
BiomartGeneRegionTrack-class3.6880.0603.788
DataTrack-class0.7760.0140.795
DisplayPars-class0.0220.0010.024
GeneRegionTrack-class6.2480.0466.357
GenomeAxisTrack-class3.8860.0123.950
IdeogramTrack-class1.1780.0181.208
SequenceTrack-class 9.475 0.75710.365
plotTracks5.5260.0805.656