BioC 3.1: CHECK report for intansv on petty

Package: intansv

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings intansv_1.8.0.tar.gz

StartedAt: 2015-10-08 23:49:19 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:57:13 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 474.2 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 intansv_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/intansv.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.8.0’
* 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 ... [30s/30s] OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
* 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 ... [157s/157s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
methodsMerge    41.289  0.097  41.405
geneAnnotation  35.817  1.074  36.907
svAnnotation    10.717  0.262  10.983
plotChromosome  10.891  0.032  10.937
plotRegion       9.492  0.027   9.526
readDelly        8.152  0.016   8.178
readLumpy        6.781  0.009   6.792
readBreakDancer  6.270  0.013   6.284
readPindel       5.073  0.014   5.087
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘rtracklayer’
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/intansv.Rcheck/00check.log’
for details.

* installing *source* package ‘intansv’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (intansv)

name	user	system	elapsed
geneAnnotation	35.817	1.074	36.907
methodsMerge	41.289	0.097	41.405
plotChromosome	10.891	0.032	10.937
plotRegion	9.492	0.027	9.526
readBreakDancer	6.270	0.013	6.284
readCnvnator	1.312	0.003	1.316
readDelly	8.152	0.016	8.178
readLumpy	6.781	0.009	6.792
readPindel	5.073	0.014	5.087
readSoftSearch	0.532	0.002	0.534
readSvseq	1.554	0.003	1.556
svAnnotation	10.717	0.262	10.983