BioC 3.5: CHECK report for basecallQC on veracruz2

Package: basecallQC

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings basecallQC_1.0.1.tar.gz

StartedAt: 2017-10-18 00:45:09 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:51:05 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 355.9 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/basecallQC.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 ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.0.1’
* 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             17.039  0.318  17.949
passFilterBoxplot      9.009  0.048   9.299
basecallQC             8.737  0.065   9.076
passFilterTileplot     8.717  0.050   8.980
demuxBarplot           8.661  0.060   9.055
demuxBoxplot           8.513  0.046   8.845
summaryConvStatsTable  8.376  0.069   8.715
baseCallMetrics        8.257  0.105   8.607
passFilterBar          8.110  0.051   8.423
summaryDemuxTable      7.868  0.061   8.187
makeFQTable            7.246  0.068   7.558
* 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-3.5-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	0.531	0.030	0.581
baseCallMetrics	8.257	0.105	8.607
basecallQC	8.737	0.065	9.076
createBCLcommand	1.007	0.007	1.035
createBasemasks	0.836	0.004	0.883
demultiplexMetrics	0.179	0.002	0.185
demuxBarplot	8.661	0.060	9.055
demuxBoxplot	8.513	0.046	8.845
indexlengths	0.033	0.001	0.034
interOpsReport	0.021	0.000	0.024
makeFQTable	7.246	0.068	7.558
passFilterBar	8.110	0.051	8.423
passFilterBoxplot	9.009	0.048	9.299
passFilterTileplot	8.717	0.050	8.980
readlengths	0.049	0.001	0.052
reportBCL	17.039	0.318	17.949
summaryConvStatsTable	8.376	0.069	8.715
summaryDemuxTable	7.868	0.061	8.187
validateBCLSheet	0.136	0.001	0.146