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BioC 2.14: CHECK report for Gviz on morelia

This page was generated on 2014-10-08 09:05:24 -0700 (Wed, 08 Oct 2014).

Package 375/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.8.4
Florian Hahne
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Gviz
Last Changed Rev: 92685 / Revision: 95116
Last Changed Date: 2014-07-21 13:53:02 -0700 (Mon, 21 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: Gviz
Version: 1.8.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Gviz_1.8.4.tar.gz
StartedAt: 2014-10-07 23:24:33 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:30:49 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 375.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Gviz_1.8.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Gviz.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.8.4’
* 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 ... [30s/30s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [71s/71s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
AlignmentsTrack              13.529  0.991  14.573
GeneRegionTrack-class         9.871  0.047   9.974
plotTracks                    7.362  0.047   7.415
AnnotationTrack-class         7.184  0.032   7.221
BiomartGeneRegionTrack-class  5.741  0.077   5.823
GenomeAxisTrack-class         5.461  0.014   5.481
* 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

Gviz.Rcheck/00install.out:

* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘subset’ from package ‘base’ in package ‘Gviz’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘Gviz’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Gviz)

Gviz.Rcheck/Gviz-Ex.timings:

nameusersystemelapsed
AlignedReadTrack-class2.2760.0482.326
AlignmentsTrack13.529 0.99114.573
AnnotationTrack-class7.1840.0327.221
BiomartGeneRegionTrack-class5.7410.0775.823
DataTrack-class0.9770.0160.993
DisplayPars-class0.0510.0020.052
GeneRegionTrack-class9.8710.0479.974
GenomeAxisTrack-class5.4610.0145.481
IdeogramTrack-class0.4230.0030.427
SequenceTrack-class3.7320.3354.079
plotTracks7.3620.0477.415