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BioC 3.5: CHECK report for MBASED on tokay2

This page was generated on 2017-08-16 13:23:36 -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: rm -rf MBASED.buildbin-libdir MBASED.Rcheck && mkdir MBASED.buildbin-libdir MBASED.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MBASED.buildbin-libdir MBASED_1.10.0.tar.gz >MBASED.Rcheck\00install.out 2>&1 && cp MBASED.Rcheck\00install.out MBASED-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MBASED.buildbin-libdir --install="check:MBASED-install.out" --force-multiarch --no-vignettes --timings MBASED_1.10.0.tar.gz
StartedAt: 2017-08-16 00:59:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:05:10 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 316.0 seconds
RetCode: 0
Status:  OK  
CheckDir: MBASED.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MBASED.buildbin-libdir MBASED.Rcheck && mkdir MBASED.buildbin-libdir MBASED.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MBASED.buildbin-libdir MBASED_1.10.0.tar.gz >MBASED.Rcheck\00install.out 2>&1 && cp MBASED.Rcheck\00install.out MBASED-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MBASED.buildbin-libdir --install="check:MBASED-install.out" --force-multiarch --no-vignettes --timings MBASED_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MBASED.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MBASED.Rcheck/00check.log'
for details.


MBASED.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'MBASED' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MBASED' as MBASED_1.10.0.zip
* DONE (MBASED)

MBASED.Rcheck/examples_i386/MBASED-Ex.timings:

nameusersystemelapsed
FreemanTukeyFunctions0.770.070.82
MBASEDMetaAnalysis0.010.000.02
MBASEDMetaAnalysisGetMeansAndSEs0.020.000.01
MBASEDVectorizedMetaprop0.080.000.08
MBASEDVectorizedPropDiffTest0.030.000.03
betaParametrizationConverters0.030.000.04
estimateMAF1s0.130.000.12
estimateMAF2s0.160.000.15
generatingBetaBinomialCounts000
getPFinal000
getSimulationPvalue0.010.000.02
logLikelihoodCalculator1s000
logLikelihoodCalculator2s000
maxLogLikelihoodCalculator1s000
maxLogLikelihoodCalculator2s000
runMBASED000
runMBASED1s000
runMBASED1s1aseID000
runMBASED2s000
runMBASED2s1aseID000
shiftAndAttenuateProportions000

MBASED.Rcheck/examples_x64/MBASED-Ex.timings:

nameusersystemelapsed
FreemanTukeyFunctions1.530.011.55
MBASEDMetaAnalysis000
MBASEDMetaAnalysisGetMeansAndSEs0.030.000.03
MBASEDVectorizedMetaprop0.170.000.17
MBASEDVectorizedPropDiffTest0.080.000.08
betaParametrizationConverters0.110.000.11
estimateMAF1s0.30.00.3
estimateMAF2s0.340.000.34
generatingBetaBinomialCounts0.010.000.02
getPFinal000
getSimulationPvalue0.040.000.03
logLikelihoodCalculator1s000
logLikelihoodCalculator2s000
maxLogLikelihoodCalculator1s000
maxLogLikelihoodCalculator2s000
runMBASED000
runMBASED1s000
runMBASED1s1aseID000
runMBASED2s000
runMBASED2s1aseID000
shiftAndAttenuateProportions000