BioC 3.0: CHECK report for intansv on oaxaca

Package: intansv

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch intansv_1.6.2.tar.gz

StartedAt: 2015-04-10 00:39:00 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:47:49 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 528.4 seconds

RetCode: 0

Status:  OK

CheckDir: intansv.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch intansv_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/intansv.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.6.2’
* 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 ... [28s/28s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
* 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 loading without being on the library search path ... 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 ... NOTE
plotChromosome: no visible global function definition for
  ‘seqlengths<-’
plotChromosome: no visible global function definition for ‘seqlengths’
plotChromosome: no visible global function definition for ‘aes’
plotRegion: no visible global function definition for ‘seqlengths<-’
plotRegion: no visible global function definition for ‘aes_string’
* 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 ... [207s/212s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
methodsMerge    53.469  0.125  54.657
geneAnnotation  37.911  0.695  39.243
svAnnotation    16.082  0.201  16.907
plotChromosome  14.984  0.041  15.484
readDelly       14.858  0.041  15.202
plotRegion      14.732  0.031  15.122
readLumpy       12.151  0.020  12.371
readBreakDancer 10.738  0.024  10.925
readPindel       9.562  0.031   9.825
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/intansv.Rcheck/00check.log’
for details.

* 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	37.911	0.695	39.243
methodsMerge	53.469	0.125	54.657
plotChromosome	14.984	0.041	15.484
plotRegion	14.732	0.031	15.122
readBreakDancer	10.738	0.024	10.925
readCnvnator	1.239	0.003	1.249
readDelly	14.858	0.041	15.202
readLumpy	12.151	0.020	12.371
readPindel	9.562	0.031	9.825
readSoftSearch	0.986	0.003	1.058
readSvseq	2.310	0.011	2.352
svAnnotation	16.082	0.201	16.907