BioC 3.0: CHECK report for intansv on perceval

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 02:54:29 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:05:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 677.0 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-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 ‘1.6.2’
* 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 ... [39s/40s] 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 ... [241s/241s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
methodsMerge    58.541  0.158  58.729
geneAnnotation  53.381  1.362  54.809
svAnnotation    16.427  0.257  16.724
plotRegion      16.544  0.063  16.627
plotChromosome  16.182  0.057  16.295
readDelly       15.555  0.039  15.604
readLumpy       13.397  0.033  13.470
readBreakDancer 12.067  0.033  12.106
readPindel       9.524  0.035   9.573
* 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	53.381	1.362	54.809
methodsMerge	58.541	0.158	58.729
plotChromosome	16.182	0.057	16.295
plotRegion	16.544	0.063	16.627
readBreakDancer	12.067	0.033	12.106
readCnvnator	1.314	0.005	1.333
readDelly	15.555	0.039	15.604
readLumpy	13.397	0.033	13.470
readPindel	9.524	0.035	9.573
readSoftSearch	0.953	0.004	0.958
readSvseq	2.219	0.009	2.231
svAnnotation	16.427	0.257	16.724