BioC 3.6: CHECK report for IntEREst on veracruz1

Package: IntEREst

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IntEREst_1.1.3.tar.gz

StartedAt: 2017-08-16 04:36:43 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:41:04 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 260.6 seconds

RetCode: 0

Status:  OK

CheckDir: IntEREst.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 IntEREst_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/IntEREst.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 ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.1.3’
* 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 ‘IntEREst’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
DEXSeqIntEREst 15.79  0.115  16.437
* 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 ‘IntEREst’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IntEREst)

name	user	system	elapsed
DEXSeqIntEREst	15.790	0.115	16.437
addAnnotation	0.046	0.001	0.046
annotateU12	2.222	0.027	2.298
attributes	0.030	0.001	0.030
boxplot-method	0.151	0.001	0.154
buildSsTypePwms	0.002	0.000	0.003
counts-method	0.063	0.000	0.065
eBayesInterest	0.095	0.001	0.097
exactTestInterest	0.661	0.002	0.686
getRepeatTable	0.000	0.000	0.001
glmInterest	0.318	0.002	0.321
interest	2.032	0.011	2.098
interest.sequential	1.954	0.011	2.024
interestResult	0.016	0.001	0.017
intexIndex	0.005	0.000	0.004
lfc	0.584	0.001	0.611
mergeInterestResult	0.219	0.001	0.223
plot-method	0.281	0.002	0.295
qlfInterest	0.312	0.001	0.320
readInterestResults	0.036	0.002	0.039
referencePrepare	1.943	0.005	2.001
subInterestResult	0.022	0.001	0.023
treatInterest	0.130	0.002	0.141
u12Boxplot	0.047	0.001	0.052
u12BoxplotNb	0.075	0.000	0.080
u12DensityPlot	0.452	0.009	0.466
u12Index	0.008	0.001	0.008
u12NbIndex	0.083	0.001	0.089
unionRefTr	0.087	0.000	0.087
updateRowDataCol	0.043	0.001	0.044