BioC 3.5: CHECK report for ATACseqQC on veracruz2

Package: ATACseqQC

Version: 1.0.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ATACseqQC_1.0.5.tar.gz

StartedAt: 2017-10-18 00:36:44 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:46:04 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 559.6 seconds

RetCode: 0

Status:  OK

CheckDir: ATACseqQC.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 ATACseqQC_1.0.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACseqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ATACseqQC’ version ‘1.0.5’
* 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 ‘ATACseqQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   7.5Mb
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
enrichedFragments     119.893  2.284 125.644
splitBam              112.184  2.242 117.760
factorFootprints       26.663  0.689  28.230
shiftGAlignmentsList   25.833  0.524  27.082
splitGAlignmentsByCut   6.661  0.781   7.701
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.

* installing *source* package ‘ATACseqQC’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ATACseqQC)

name	user	system	elapsed
enrichedFragments	119.893	2.284	125.644
factorFootprints	26.663	0.689	28.230
fragSizeDist	0.385	0.007	0.410
plotFootprints	1.348	0.118	1.531
readBamFile	1.214	0.069	1.303
shiftGAlignmentsList	25.833	0.524	27.082
splitBam	112.184	2.242	117.760
splitGAlignmentsByCut	6.661	0.781	7.701
writeListOfGAlignments	0.331	0.008	0.344