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BioC 3.5: CHECK report for funtooNorm on toluca2

This page was generated on 2017-04-23 14:42:34 -0400 (Sun, 23 Apr 2017).

Package 484/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 0.99.11
Kathleen Klein
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/funtooNorm
Last Changed Rev: 125712 / Revision: 129046
Last Changed Date: 2017-01-05 18:10:15 -0500 (Thu, 05 Jan 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: funtooNorm
Version: 0.99.11
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings funtooNorm_0.99.11.tar.gz
StartedAt: 2017-04-23 04:03:07 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 04:10:19 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 432.7 seconds
RetCode: 0
Status:  OK 
CheckDir: funtooNorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings funtooNorm_0.99.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/funtooNorm.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.11’
* 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 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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
plotValidationGraph   32.410  0.962  33.835
getNormBeta           24.746  1.492  26.463
funtooNorm            24.060  1.352  25.636
getSnpM               23.091  1.367  24.949
getNormM              22.205  1.431  23.908
fromRGChannelSet      13.865  1.069  15.047
getGRanges             6.679  0.878   7.657
getRawBeta             5.888  0.879   6.818
show-SampleSet-method  4.681  0.752   5.491
* 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

funtooNorm.Rcheck/00install.out:

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

funtooNorm.Rcheck/funtooNorm-Ex.timings:

nameusersystemelapsed
SampleSet-class0.0020.0010.002
agreement0.0020.0000.002
fromRGChannelSet13.865 1.06915.047
funtooNorm24.060 1.35225.636
getGRanges6.6790.8787.657
getNormBeta24.746 1.49226.463
getNormM22.205 1.43123.908
getRawBeta5.8880.8796.818
getSnpM23.091 1.36724.949
plotValidationGraph32.410 0.96233.835
show-SampleSet-method4.6810.7525.491