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BioC 3.5: CHECK report for TVTB on toluca2

This page was generated on 2017-04-23 14:42:20 -0400 (Sun, 23 Apr 2017).

Package 1338/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TVTB 1.1.12
Kevin Rue-Albrecht
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TVTB
Last Changed Rev: 128496 / Revision: 129046
Last Changed Date: 2017-04-10 16:45:13 -0400 (Mon, 10 Apr 2017)
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 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TVTB
Version: 1.1.12
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TVTB_1.1.12.tar.gz
StartedAt: 2017-04-23 11:00:02 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 11:07:15 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 433.0 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_1.1.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TVTB.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.1.12’
* 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 6.524  0.222   8.111
* 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-class0.0050.0010.005
TVTBParam-class0.3530.0150.380
VcfBasicRules-class3.9080.1184.917
VcfFilterRules-class2.2520.1223.003
addCountGenos-methods0.5500.0760.783
addFrequencies-methods0.5130.0700.585
addOverallFrequencies-methods0.4890.0810.570
addPhenoLevelFrequencies-methods0.5880.0740.662
autodetectGenotypes0.4470.0720.520
countGenos-methods0.4690.0760.546
dropInfo-methods0.5060.0750.582
pairsInfo-methods3.9570.0864.296
plotInfo-methods6.5240.2228.111
readVcf-methods0.3790.0260.556
tSVE0.0010.0000.001
variantsInSamples-methods0.5460.0840.748
vepInPhenoLevel-methods0.7830.0790.874