BioC 3.6: CHECK report for ATACseqQC on veracruz1

Package: ATACseqQC

Version: 1.1.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ATACseqQC_1.1.5.tar.gz

StartedAt: 2017-08-16 00:03:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:15:19 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 703.2 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_1.1.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.1.5’
* 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  8.8Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    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     132.190  2.189 138.192
splitBam              112.069  1.851 117.287
factorFootprints       43.701  0.665  45.555
shiftGAlignmentsList   25.148  0.445  26.401
splitGAlignmentsByCut   8.190  0.894   9.459
* 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-3.6-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	132.190	2.189	138.192
factorFootprints	43.701	0.665	45.555
fragSizeDist	0.403	0.007	0.418
plotFootprints	1.426	0.122	1.623
readBamFile	1.200	0.064	1.313
shiftGAlignmentsList	25.148	0.445	26.401
splitBam	112.069	1.851	117.287
splitGAlignmentsByCut	8.190	0.894	9.459
writeListOfGAlignments	0.454	0.009	0.477