BioC 3.3: CHECK report for intansv on linux2.bioconductor.org

Package: intansv

Version: 1.9.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings intansv_1.9.1.tar.gz

StartedAt: 2015-10-27 05:03:04 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:07:41 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 277.1 seconds

RetCode: 0

Status:  OK

CheckDir: intansv.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings intansv_1.9.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/intansv.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.9.1’
* 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 ... [19s/19s] 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’
Undefined global functions or variables:
  aes aes_string seqlengths seqlengths<-
* 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 ... [84s/88s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
methodsMerge   22.808  0.008  24.028
geneAnnotation 22.520  0.111  24.381
svAnnotation    5.265  0.000   5.278
* 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
  ‘/home/biocbuild/bbs-3.3-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	22.520	0.111	24.381
methodsMerge	22.808	0.008	24.028
plotChromosome	4.091	0.000	4.094
plotRegion	4.318	0.000	4.320
readBreakDancer	2.99	0.00	2.99
readCnvnator	0.544	0.000	0.545
readDelly	3.883	0.000	3.882
readLumpy	3.029	0.000	3.030
readPindel	3.538	0.004	4.165
readSoftSearch	0.393	0.000	0.553
readSvseq	1.114	0.000	1.355
svAnnotation	5.265	0.000	5.278