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BioC 3.5: CHECK report for MBASED on veracruz2

This page was generated on 2017-08-16 13:32:17 -0400 (Wed, 16 Aug 2017).

Package 764/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBASED 1.10.0
Oleg Mayba
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MBASED
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: MBASED
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MBASED_1.10.0.tar.gz
StartedAt: 2017-08-16 04:53:35 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:56:59 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 204.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MBASED.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MBASED_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MBASED.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBASED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MBASED’ version ‘1.10.0’
* 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 ‘MBASED’ 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
MBASEDMetaAnalysis: no visible global function definition for ‘pchisq’
MBASEDMetaAnalysis: no visible global function definition for ‘pnorm’
maxLogLikelihoodCalculator1s: no visible global function definition for
  ‘optimize’
maxLogLikelihoodCalculator2s: no visible global function definition for
  ‘optimize’
runMBASED: no visible global function definition for ‘is’
runMBASED1s: no visible global function definition for ‘is’
runMBASED2s: no visible global function definition for ‘is’
vectorizedRbetabinomAB: no visible global function definition for
  ‘rbeta’
vectorizedRbetabinomAB: no visible global function definition for
  ‘rbinom’
vectorizedRbetabinomMR: no visible global function definition for
  ‘rbeta’
vectorizedRbetabinomMR: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  is optimize pchisq pnorm rbeta rbinom
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "optimize", "pchisq", "pnorm", "rbeta", "rbinom")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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/MBASED.Rcheck/00check.log’
for details.


MBASED.Rcheck/00install.out:

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

MBASED.Rcheck/MBASED-Ex.timings:

nameusersystemelapsed
FreemanTukeyFunctions0.9660.0421.042
MBASEDMetaAnalysis0.0030.0000.004
MBASEDMetaAnalysisGetMeansAndSEs0.0240.0000.025
MBASEDVectorizedMetaprop0.1310.0010.135
MBASEDVectorizedPropDiffTest0.0600.0000.065
betaParametrizationConverters0.0700.0000.074
estimateMAF1s0.2300.0010.244
estimateMAF2s0.2910.0010.298
generatingBetaBinomialCounts0.0010.0000.001
getPFinal0.0020.0000.002
getSimulationPvalue0.0320.0010.034
logLikelihoodCalculator1s0.0010.0000.001
logLikelihoodCalculator2s0.0020.0000.001
maxLogLikelihoodCalculator1s0.0010.0010.001
maxLogLikelihoodCalculator2s0.0020.0000.002
runMBASED000
runMBASED1s0.0000.0010.001
runMBASED1s1aseID0.0000.0000.001
runMBASED2s0.0010.0000.001
runMBASED2s1aseID0.0010.0010.001
shiftAndAttenuateProportions0.0010.0000.002