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BioC 3.5: CHECK report for PathoStat on veracruz2

This page was generated on 2017-08-16 13:35:08 -0400 (Wed, 16 Aug 2017).

Package 951/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PathoStat 1.2.0
Solaiappan Manimaran
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/PathoStat
Last Changed Rev: 129482 / Revision: 131943
Last Changed Date: 2017-05-08 23:37:35 -0400 (Mon, 08 May 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  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PathoStat
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathoStat_1.2.0.tar.gz
StartedAt: 2017-08-16 06:17:15 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:22:30 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 314.7 seconds
RetCode: 0
Status:  OK 
CheckDir: PathoStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathoStat_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PathoStat.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathoStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathoStat’ version ‘1.2.0’
* 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 ‘PathoStat’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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
loadPathoscopeReports 4.725  0.557   5.406
createPathoStat       1.428  0.049  17.412
* 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

PathoStat.Rcheck/00install.out:

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

PathoStat.Rcheck/PathoStat-Ex.timings:

nameusersystemelapsed
coreOTU0.1170.0020.121
coreOTUModule0.0010.0000.001
coreOTUModuleUI0.6050.0030.629
coreOTUNormalize0.0750.0010.077
coreOTUQuantile0.0270.0020.028
createPathoStat 1.428 0.04917.412
findRAfromCount0.1750.0030.179
findTaxonLevel0.0800.0010.541
findTaxonMat0.2050.0022.685
findTaxonomy0.1820.0012.432
getShinyInput000
getShinyInputCombat0.0010.0000.001
getShinyInputOrig0.0010.0000.001
grepTid000
loadPathoscopeReports4.7250.5575.406
loadPstat0.0020.0010.002
log2CPM0.0270.0010.028
pathostat0.2080.0010.212
plotConfRegion1.0520.0111.106
readPathoscopeData0.0520.0040.057
runPathoStat3.9000.2674.602
savePstat0.0070.0010.008
setShinyInput000
setShinyInputCombat000
setShinyInputOrig0.0000.0000.001
sizeNormalize0.0340.0020.035