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BioC 3.5: CHECK report for BEclear on veracruz2

This page was generated on 2017-10-18 14:33:19 -0400 (Wed, 18 Oct 2017).

Package 100/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 1.8.0
Markus Merl
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/BEclear
Branch: RELEASE_3_5
Last Commit: 7a8af1e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 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: BEclear
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BEclear_1.8.0.tar.gz
StartedAt: 2017-10-18 00:52:35 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:54:13 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 98.7 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BEclear.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 ‘BEclear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEclear’ version ‘1.8.0’
* 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 ... 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 ... NOTE
BEclear : BEclear: no visible global function definition for ‘as’
BEclear : BEclear: no visible global function definition for ‘rnorm’
BEclear: no visible global function definition for ‘write.table’
calcMedians : calcMedians: no visible global function definition for
  ‘median’
calcPvalues : calcPvals: no visible global function definition for
  ‘ks.test’
calcPvalues: no visible global function definition for ‘p.adjust’
makeBoxplot: no visible global function definition for ‘par’
makeBoxplot: no visible global function definition for ‘boxplot’
makeBoxplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  as boxplot ks.test median mtext p.adjust par rnorm write.table
Consider adding
  importFrom("graphics", "boxplot", "mtext", "par")
  importFrom("methods", "as")
  importFrom("stats", "ks.test", "median", "p.adjust", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BEclear              0.802  0.044  20.289
correctBatchEffect   0.634  0.041   9.483
countValuesToPredict 0.126  0.019   6.152
makeBoxplot          0.121  0.016   6.034
clearBEgenes         0.098  0.017   6.325
* 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/BEclear.Rcheck/00check.log’
for details.


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-package2.5810.0322.660
BEclear 0.802 0.04420.289
BEclearData0.0010.0000.001
calcMedians0.0750.0010.076
calcPvalues0.1120.0010.114
calcScore0.2760.0020.279
calcSummary0.1800.0010.181
clearBEgenes0.0980.0176.325
correctBatchEffect0.6340.0419.483
countValuesToPredict0.1260.0196.152
findWrongValues0.4670.0030.477
makeBoxplot0.1210.0166.034
replaceWrongValues0.3930.0030.398