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BioC 3.5: CHECK report for basecallQC on veracruz2

This page was generated on 2017-10-18 14:35:34 -0400 (Wed, 18 Oct 2017).

Package 86/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.0.1
Thomas Carroll
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: RELEASE_3_5
Last Commit: 9b7885d
Last Changed Date: 2017-06-08 12:21:39 -0400 (Thu, 08 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


basecallQC.Rcheck/00install.out:

* 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)

basecallQC.Rcheck/basecallQC-Ex.timings:

nameusersystemelapsed
BCL2FastQparams0.5310.0300.581
baseCallMetrics8.2570.1058.607
basecallQC8.7370.0659.076
createBCLcommand1.0070.0071.035
createBasemasks0.8360.0040.883
demultiplexMetrics0.1790.0020.185
demuxBarplot8.6610.0609.055
demuxBoxplot8.5130.0468.845
indexlengths0.0330.0010.034
interOpsReport0.0210.0000.024
makeFQTable7.2460.0687.558
passFilterBar8.1100.0518.423
passFilterBoxplot9.0090.0489.299
passFilterTileplot8.7170.0508.980
readlengths0.0490.0010.052
reportBCL17.039 0.31817.949
summaryConvStatsTable8.3760.0698.715
summaryDemuxTable7.8680.0618.187
validateBCLSheet0.1360.0010.146