BioC 2.13: CHECK report for intansv on perceval

Package: intansv

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch intansv_1.2.0.tar.gz

StartedAt: 2014-04-05 02:07:51 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:18:57 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 666.4 seconds

RetCode: 0

Status:  OK

CheckDir: intansv.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/intansv.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.2.0’
* 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 ‘intansv’ can be installed ... [37s/39s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [303s/307s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneAnnotation  74.503 15.873  92.050
methodsMerge    63.545  2.578  67.149
plotRegion      24.764  0.759  25.858
plotChromosome  23.796  0.755  24.728
svAnnotation    23.032  1.024  24.329
readDelly       21.102  0.636  21.946
readBreakDancer 13.982  0.424  14.678
readPindel       7.952  0.203   8.210
* 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

* installing *source* package ‘intansv’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (intansv)

name	user	system	elapsed
geneAnnotation	74.503	15.873	92.050
methodsMerge	63.545	2.578	67.149
plotChromosome	23.796	0.755	24.728
plotRegion	24.764	0.759	25.858
readBreakDancer	13.982	0.424	14.678
readCnvnator	1.468	0.016	1.545
readDelly	21.102	0.636	21.946
readLumpy	2.405	0.063	2.475
readPindel	7.952	0.203	8.210
readSoftSearch	1.119	0.022	1.143
readSvseq	3.425	0.060	3.494
svAnnotation	23.032	1.024	24.329