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BioC 3.5: CHECK report for TVTB on oaxaca

This page was generated on 2017-03-04 16:53:29 -0500 (Sat, 04 Mar 2017).

Package 1301/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TVTB 1.1.10
Kevin Rue-Albrecht
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TVTB
Last Changed Rev: 124263 / Revision: 127142
Last Changed Date: 2016-11-18 07:22:14 -0500 (Fri, 18 Nov 2016)
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 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  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 

Summary

Package: TVTB
Version: 1.1.10
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TVTB_1.1.10.tar.gz
StartedAt: 2017-03-04 10:16:23 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 10:22:21 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 357.8 seconds
RetCode: 0
Status:  OK 
CheckDir: TVTB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TVTB_1.1.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TVTB.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.1.10’
* 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 ‘TVTB’ 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotInfo-methods 5.474  0.272   6.981
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

TVTB.Rcheck/00install.out:

* installing *source* package ‘TVTB’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TVTB)

TVTB.Rcheck/TVTB-Ex.timings:

nameusersystemelapsed
Genotypes-class0.0050.0000.005
TVTBParam-class0.4160.0040.430
VcfBasicRules-class3.8260.1084.018
VcfFilterRules-class3.0640.1503.217
addCountGenos-methods0.5840.0820.671
addFrequencies-methods0.6180.0950.716
addOverallFrequencies-methods0.5800.0840.664
addPhenoLevelFrequencies-methods0.7130.0820.796
autodetectGenotypes0.5000.0740.576
countGenos-methods0.4670.0630.531
dropInfo-methods0.3650.0550.420
pairsInfo-methods3.9040.0664.094
plotInfo-methods5.4740.2726.981
readVcf-methods0.2950.0250.320
tSVE0.0000.0000.001
variantsInSamples-methods0.3320.0510.383
vepInPhenoLevel-methods0.6230.0700.693