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BioC 3.1: CHECK report for BEclear on petty

This page was generated on 2015-10-09 09:37:40 -0700 (Fri, 09 Oct 2015).

Package 79/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 1.0.0
Markus Merl
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BEclear
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BEclear
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BEclear_1.0.0.tar.gz
StartedAt: 2015-10-08 21:37:44 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 21:41:54 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 249.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BEclear.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BEclear_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BEclear.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEclear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEclear’ version ‘1.0.0’
* 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 ‘BEclear’ can be installed ... [7s/7s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/173s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BEclear-package      5.472  0.027   5.508
BEclear              0.310  0.069  65.821
correctBatchEffect   0.306  0.051  66.141
makeBoxplot          0.205  0.028   9.901
countValuesToPredict 0.177  0.025   9.694
clearBEgenes         0.162  0.026   9.960
* 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

BEclear.Rcheck/00install.out:

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

BEclear.Rcheck/BEclear-Ex.timings:

nameusersystemelapsed
BEclear-package5.4720.0275.508
BEclear 0.310 0.06965.821
BEclearData0.0020.0000.001
calcMedians0.1380.0000.140
calcPvalues0.3340.0010.336
calcScore0.4620.0020.463
calcSummary0.4100.0010.412
clearBEgenes0.1620.0269.960
correctBatchEffect 0.306 0.05166.141
countValuesToPredict0.1770.0259.694
findWrongValues0.7430.0090.751
makeBoxplot0.2050.0289.901
replaceWrongValues0.9170.0070.925