BioC 3.5: CHECK report for PathoStat on veracruz2

Package: PathoStat

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathoStat_1.2.1.tar.gz

StartedAt: 2017-10-18 07:04:19 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:09:34 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 315.3 seconds

RetCode: 0

Status:  OK

CheckDir: PathoStat.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathoStat_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PathoStat.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.1’
* 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 6.992  0.832   8.086
createPathoStat       1.357  0.049  16.657
* 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

* 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)

name	user	system	elapsed
coreOTU	0.059	0.002	0.063
coreOTUModule	0.000	0.000	0.001
coreOTUModuleUI	0.180	0.003	0.190
coreOTUNormalize	0.523	0.004	0.537
coreOTUQuantile	0.028	0.001	0.029
createPathoStat	1.357	0.049	16.657
findRAfromCount	0.177	0.002	0.182
findTaxonLevel	0.058	0.002	0.515
findTaxonMat	0.172	0.003	2.608
findTaxonomy	0.179	0.002	2.442
getShinyInput	0.001	0.000	0.001
getShinyInputCombat	0.000	0.000	0.001
getShinyInputOrig	0	0	0
grepTid	0	0	0
loadPathoscopeReports	6.992	0.832	8.086
loadPstat	0.002	0.001	0.003
log2CPM	0.030	0.001	0.034
pathostat	0.302	0.002	0.308
plotConfRegion	1.209	0.016	1.263
readPathoscopeData	0.062	0.005	0.068
runPathoStat	3.976	0.266	4.692
savePstat	0.005	0.001	0.007
setShinyInput	0.000	0.000	0.001
setShinyInputCombat	0.001	0.000	0.001
setShinyInputOrig	0.001	0.000	0.001
sizeNormalize	0.032	0.001	0.033