BioC 3.6: CHECK report for basecallQC on veracruz1

Package: basecallQC

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings basecallQC_1.1.1.tar.gz

StartedAt: 2017-08-16 00:10:05 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:16:27 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 381.8 seconds

RetCode: 0

Status:  OK

CheckDir: basecallQC.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 basecallQC_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/basecallQC.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 ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.1.1’
* 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 ‘basecallQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.8Mb
* 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
reportBCL             18.674  0.296  19.883
summaryDemuxTable      9.988  0.051  10.292
demuxBoxplot           9.689  0.032  10.029
basecallQC             9.413  0.041   9.749
passFilterTileplot     9.381  0.030   9.778
passFilterBoxplot      9.383  0.026   9.698
summaryConvStatsTable  9.330  0.023   9.511
passFilterBar          9.137  0.025   9.430
makeFQTable            9.080  0.027   9.416
demuxBarplot           9.032  0.038   9.341
baseCallMetrics        8.665  0.073   8.996
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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/basecallQC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
BCL2FastQparams	0.494	0.017	0.531
baseCallMetrics	8.665	0.073	8.996
basecallQC	9.413	0.041	9.749
createBCLcommand	0.912	0.003	0.958
createBasemasks	0.794	0.002	0.808
demultiplexMetrics	0.155	0.001	0.163
demuxBarplot	9.032	0.038	9.341
demuxBoxplot	9.689	0.032	10.029
indexlengths	0.055	0.001	0.060
interOpsReport	0.034	0.000	0.035
makeFQTable	9.080	0.027	9.416
passFilterBar	9.137	0.025	9.430
passFilterBoxplot	9.383	0.026	9.698
passFilterTileplot	9.381	0.030	9.778
readlengths	0.057	0.001	0.057
reportBCL	18.674	0.296	19.883
summaryConvStatsTable	9.330	0.023	9.511
summaryDemuxTable	9.988	0.051	10.292
validateBCLSheet	0.178	0.001	0.193