BioC 3.6: CHECK report for INSPEcT on malbec1

Package: INSPEcT

Version: 1.7.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.7.1.tar.gz

StartedAt: 2017-08-16 00:05:28 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:10:26 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 298.6 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.7.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/INSPEcT.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.7.1’
* 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 ‘INSPEcT’ 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
modelRates     25.464  0.060  25.541
rocThresholds  21.816  0.028  21.860
makeSimDataset  7.968  0.260   8.355
compareSteady   6.972  0.132   7.138
makeSimModel    6.204  0.228   6.577
makeRPKMs       5.136  0.128  11.489
* 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 ‘INSPEcT’ ...
** 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 (INSPEcT)

name	user	system	elapsed
AIC-INSPEcT-method	0.008	0.000	0.009
Extract	0.116	0.000	0.116
INSPEcT_diffsteady-class	2.380	0.080	2.462
chisqmodel	0.068	0.004	0.070
chisqtest	0.004	0.004	0.008
combine	0.240	0.024	0.263
compareSteady	6.972	0.132	7.138
geneClass	0.120	0.004	0.125
getModel	0.004	0.000	0.006
inHeatmap	0.160	0.000	0.157
labeledSF	0.008	0.000	0.007
logLik	0.004	0.004	0.008
makeModelRates	0.556	0.000	0.558
makeRPKMs	5.136	0.128	11.489
makeSimDataset	7.968	0.260	8.355
makeSimModel	6.204	0.228	6.577
modelRates	25.464	0.060	25.541
modelingParams	0.012	0.000	0.014
nGenes	0.008	0.000	0.007
nTpts	0.008	0.000	0.007
newINSPEcT	1.556	0.004	1.561
plotGene	0.028	0.000	0.026
plotMA	1.136	0.016	1.170
ratePvals	0.060	0.000	0.057
ratesFirstGuess	1.624	0.012	1.638
ratesFirstGuessVar	1.668	0.012	1.680
removeModel	0.068	0.000	0.070
rocCurve	2.464	0.024	2.490
rocThresholds	21.816	0.028	21.860
sfPlot	1.632	0.000	1.634
split	0.048	0.000	0.051
testingParams	0.888	0.000	0.888
totalSF	0.004	0.000	0.007
tpts	0.004	0.000	0.006
viewModelRates	0.008	0.000	0.007