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CHECK report for funtooNorm on malbec2

This page was generated on 2019-04-09 11:47:17 -0400 (Tue, 09 Apr 2019).

Package 587/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 1.7.0
Kathleen Klein
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/funtooNorm
Branch: master
Last Commit: fc4221f
Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: funtooNorm
Version: 1.7.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings funtooNorm_1.7.0.tar.gz
StartedAt: 2019-04-09 00:35:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:42:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 387.8 seconds
RetCode: 0
Status:  OK 
CheckDir: funtooNorm.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings funtooNorm_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/funtooNorm.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘funtooNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘funtooNorm’ version ‘1.7.0’
* 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 ‘funtooNorm’ can be installed ... OK
* checking installed package size ... OK
* 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 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotValidationGraph 23.779  0.088  23.879
getNormBeta         21.228  0.064  21.342
getSnpM             19.662  0.060  19.737
funtooNorm          18.322  0.160  18.532
getNormM            16.896  0.056  17.014
fromRGChannelSet    12.784  0.404  13.748
getGRanges           7.149  0.044   7.196
getRawBeta           6.749  0.004   6.753
* 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: OK


Installation output

funtooNorm.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL funtooNorm
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘funtooNorm’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (funtooNorm)

Tests output


Example timings

funtooNorm.Rcheck/funtooNorm-Ex.timings

nameusersystemelapsed
SampleSet-class0.0010.0000.002
agreement0.0020.0000.001
fromRGChannelSet12.784 0.40413.748
funtooNorm18.322 0.16018.532
getGRanges7.1490.0447.196
getNormBeta21.228 0.06421.342
getNormM16.896 0.05617.014
getRawBeta6.7490.0046.753
getSnpM19.662 0.06019.737
plotValidationGraph23.779 0.08823.879
show-SampleSet-method4.5040.0004.504