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BioC 3.2: CHECK report for MBASED on zin1

This page was generated on 2016-04-23 10:14:03 -0700 (Sat, 23 Apr 2016).

Package 601/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBASED 1.4.0
Oleg Mayba
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MBASED
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MBASED
Version: 1.4.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MBASED_1.4.0.tar.gz
StartedAt: 2016-04-23 02:30:40 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:32:47 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 127.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MBASED.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MBASED_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MBASED.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.4.0’
* 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 ... [8s/8s] 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 ... OK
* 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 ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [45s/45s]
 [45s/45s] 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: OK

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
FreemanTukeyFunctions0.7620.0120.774
MBASEDMetaAnalysis0.0020.0000.002
MBASEDMetaAnalysisGetMeansAndSEs0.0010.0000.001
MBASEDVectorizedMetaprop0.0040.0000.004
MBASEDVectorizedPropDiffTest0.0020.0000.003
betaParametrizationConverters0.0010.0000.001
estimateMAF1s0.0060.0000.006
estimateMAF2s0.0040.0000.005
generatingBetaBinomialCounts0.0020.0000.001
getPFinal0.0010.0000.001
getSimulationPvalue0.0010.0000.000
logLikelihoodCalculator1s0.0010.0000.001
logLikelihoodCalculator2s0.0010.0000.001
maxLogLikelihoodCalculator1s0.0000.0000.001
maxLogLikelihoodCalculator2s0.0020.0000.001
runMBASED000
runMBASED1s0.0000.0000.001
runMBASED1s1aseID0.0010.0000.001
runMBASED2s0.0000.0040.000
runMBASED2s1aseID0.0000.0000.001
shiftAndAttenuateProportions0.0010.0000.001