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CHECK report for MBASED on celaya2

This page was generated on 2019-10-16 12:53:48 -0400 (Wed, 16 Oct 2019).

Package 930/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBASED 1.18.0
Oleg Mayba
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MBASED
Branch: RELEASE_3_9
Last Commit: 4a22826
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MBASED
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MBASED.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MBASED_1.18.0.tar.gz
StartedAt: 2019-10-16 04:18:53 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:23:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 291.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MBASED.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MBASED.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MBASED_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MBASED.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 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 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-3.9-bioc/meat/MBASED.Rcheck/00check.log’
for details.



Installation output

MBASED.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MBASED
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MBASED’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (MBASED)

Tests output

MBASED.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Welcome to Bioconductor

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


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum



RUNIT TEST PROTOCOL -- Wed Oct 16 04:23:35 2019 
*********************************************** 
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 
 80.586   2.232  83.211 

Example timings

MBASED.Rcheck/MBASED-Ex.timings

nameusersystemelapsed
FreemanTukeyFunctions1.6600.0741.790
MBASEDMetaAnalysis0.0070.0010.008
MBASEDMetaAnalysisGetMeansAndSEs0.0020.0010.002
MBASEDVectorizedMetaprop0.0100.0020.011
MBASEDVectorizedPropDiffTest0.0050.0010.007
betaParametrizationConverters0.0010.0010.003
estimateMAF1s0.0130.0010.013
estimateMAF2s0.0080.0010.008
generatingBetaBinomialCounts0.0020.0010.002
getPFinal0.0020.0010.002
getSimulationPvalue0.0010.0010.001
logLikelihoodCalculator1s0.0000.0010.002
logLikelihoodCalculator2s0.0010.0010.002
maxLogLikelihoodCalculator1s0.0010.0000.001
maxLogLikelihoodCalculator2s0.0010.0000.002
runMBASED0.0000.0000.001
runMBASED1s0.0000.0000.001
runMBASED1s1aseID0.0000.0000.001
runMBASED2s0.0010.0010.001
runMBASED2s1aseID0.0010.0000.000
shiftAndAttenuateProportions0.0020.0010.003