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CHECK report for MBASED on malbec2

This page was generated on 2018-10-17 08:26:33 -0400 (Wed, 17 Oct 2018).

Package 842/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBASED 1.14.0
Oleg Mayba
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/MBASED
Branch: RELEASE_3_7
Last Commit: 9e8b9d8
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MBASED
Version: 1.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MBASED.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MBASED_1.14.0.tar.gz
StartedAt: 2018-10-16 01:42:56 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:45:21 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 144.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MBASED.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MBASED.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MBASED_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MBASED.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/MBASED.Rcheck/00check.log’
for details.



Installation output

MBASED.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MBASED
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘MBASED’ ...
** 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
* DONE (MBASED)

Tests output

MBASED.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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



RUNIT TEST PROTOCOL -- Tue Oct 16 01:45:18 2018 
*********************************************** 
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 
 40.176   0.488  40.758 

Example timings

MBASED.Rcheck/MBASED-Ex.timings

nameusersystemelapsed
FreemanTukeyFunctions0.6160.0600.677
MBASEDMetaAnalysis0.0040.0000.002
MBASEDMetaAnalysisGetMeansAndSEs0.0000.0000.001
MBASEDVectorizedMetaprop0.0080.0000.005
MBASEDVectorizedPropDiffTest0.0040.0000.003
betaParametrizationConverters0.0000.0000.001
estimateMAF1s0.0080.0000.007
estimateMAF2s0.0040.0000.005
generatingBetaBinomialCounts0.0000.0000.001
getPFinal0.0040.0000.001
getSimulationPvalue0.0000.0000.001
logLikelihoodCalculator1s0.0000.0000.001
logLikelihoodCalculator2s000
maxLogLikelihoodCalculator1s0.0000.0000.001
maxLogLikelihoodCalculator2s0.0000.0040.001
runMBASED000
runMBASED1s000
runMBASED1s1aseID000
runMBASED2s0.0000.0000.001
runMBASED2s1aseID0.0040.0000.000
shiftAndAttenuateProportions0.0000.0000.002