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CHECK report for MBASED on tokay1

This page was generated on 2021-05-06 12:32:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MBASED package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1015/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBASED 1.24.0  (landing page)
Oleg Mayba
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MBASED
Branch: RELEASE_3_12
Last Commit: 3d1c13e
Last Changed Date: 2020-10-27 10:58:25 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MBASED
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MBASED.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MBASED_1.24.0.tar.gz
StartedAt: 2021-05-06 04:17:40 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:26:23 -0400 (Thu, 06 May 2021)
EllapsedTime: 523.5 seconds
RetCode: 0
Status:   OK   
CheckDir: MBASED.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MBASED.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MBASED_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MBASED.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.24.0'
* 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
* 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 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 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-3.12-bioc/meat/MBASED.Rcheck/00check.log'
for details.



Installation output

MBASED.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MBASED_1.24.0.tar.gz && rm -rf MBASED.buildbin-libdir && mkdir MBASED.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MBASED.buildbin-libdir MBASED_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MBASED_1.24.0.zip && rm MBASED_1.24.0.tar.gz MBASED_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 74728  100 74728    0     0  3783k      0 --:--:-- --:--:-- --:--:-- 4054k

install for i386

* installing *source* package 'MBASED' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MBASED'
    finding HTML links ... done
    FreemanTukeyFunctions                   html  
    MBASED                                  html  
    MBASEDMetaAnalysis                      html  
    MBASEDMetaAnalysisGetMeansAndSEs        html  
    MBASEDVectorizedMetaprop                html  
    MBASEDVectorizedPropDiffTest            html  
    betaParametrizationConverters           html  
    estimateMAF1s                           html  
    estimateMAF2s                           html  
    generatingBetaBinomialCounts            html  
    getPFinal                               html  
    getSimulationPvalue                     html  
    logLikelihoodCalculator1s               html  
    logLikelihoodCalculator2s               html  
    maxLogLikelihoodCalculator1s            html  
    maxLogLikelihoodCalculator2s            html  
    runMBASED                               html  
    runMBASED1s                             html  
    runMBASED1s1aseID                       html  
    runMBASED2s                             html  
    runMBASED2s1aseID                       html  
    shiftAndAttenuateProportions            html  
    testNumericDiff                         html  
    testQuantiles                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MBASED' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MBASED' as MBASED_1.24.0.zip
* DONE (MBASED)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MBASED' successfully unpacked and MD5 sums checked

Tests output

MBASED.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("MBASED")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians



RUNIT TEST PROTOCOL -- Thu May 06 04:23:02 2021 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MBASED RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 137.26    1.17  138.45 

MBASED.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("MBASED")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians



RUNIT TEST PROTOCOL -- Thu May 06 04:26:17 2021 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MBASED RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 193.39    1.17  194.59 

Example timings

MBASED.Rcheck/examples_i386/MBASED-Ex.timings

nameusersystemelapsed
FreemanTukeyFunctions1.160.331.49
MBASEDMetaAnalysis000
MBASEDMetaAnalysisGetMeansAndSEs000
MBASEDVectorizedMetaprop0.010.000.02
MBASEDVectorizedPropDiffTest000
betaParametrizationConverters000
estimateMAF1s0.020.000.01
estimateMAF2s0.000.010.02
generatingBetaBinomialCounts000
getPFinal000
getSimulationPvalue0.000.020.01
logLikelihoodCalculator1s000
logLikelihoodCalculator2s000
maxLogLikelihoodCalculator1s000
maxLogLikelihoodCalculator2s000
runMBASED000
runMBASED1s000
runMBASED1s1aseID000
runMBASED2s000
runMBASED2s1aseID000
shiftAndAttenuateProportions000

MBASED.Rcheck/examples_x64/MBASED-Ex.timings

nameusersystemelapsed
FreemanTukeyFunctions0.750.050.80
MBASEDMetaAnalysis000
MBASEDMetaAnalysisGetMeansAndSEs000
MBASEDVectorizedMetaprop000
MBASEDVectorizedPropDiffTest000
betaParametrizationConverters000
estimateMAF1s0.010.000.01
estimateMAF2s000
generatingBetaBinomialCounts000
getPFinal000
getSimulationPvalue000
logLikelihoodCalculator1s000
logLikelihoodCalculator2s0.020.000.02
maxLogLikelihoodCalculator1s000
maxLogLikelihoodCalculator2s000
runMBASED000
runMBASED1s000
runMBASED1s1aseID000
runMBASED2s000
runMBASED2s1aseID000
shiftAndAttenuateProportions000