BioC 2.13: CHECK report for intansv on zin1

Package: intansv

Version: 1.2.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings intansv_1.2.0.tar.gz

StartedAt: 2014-04-05 01:57:57 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:04:03 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 366.4 seconds

RetCode: 0

Status:  OK

CheckDir: intansv.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/intansv.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [21s/21s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [172s/172s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
methodsMerge    44.242  0.020  44.392
geneAnnotation  39.791  0.124  39.990
plotChromosome  15.205  0.016  15.244
plotRegion      14.997  0.000  15.026
svAnnotation    14.025  0.008  14.101
readDelly       13.357  0.004  13.385
readBreakDancer  9.081  0.000   9.096
readPindel       5.256  0.000   5.265
* 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	39.791	0.124	39.990
methodsMerge	44.242	0.020	44.392
plotChromosome	15.205	0.016	15.244
plotRegion	14.997	0.000	15.026
readBreakDancer	9.081	0.000	9.096
readCnvnator	0.908	0.000	0.910
readDelly	13.357	0.004	13.385
readLumpy	1.744	0.000	1.748
readPindel	5.256	0.000	5.265
readSoftSearch	0.768	0.000	0.767
readSvseq	1.768	0.000	1.770
svAnnotation	14.025	0.008	14.101