BioC 3.5: CHECK report for INSPEcT on malbec2

Package: INSPEcT

Version: 1.6.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.6.1.tar.gz

StartedAt: 2017-10-18 00:09:44 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:14:56 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 312.4 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/INSPEcT.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.1’
* 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     28.100  0.036  28.157
rocThresholds  22.584  0.008  22.604
makeSimDataset  7.436  0.256  13.161
compareSteady   7.368  0.160   7.576
makeSimModel    6.284  0.260  12.190
makeRPKMs       5.688  0.132   7.715
* 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	0.016	0.000	0.016
Extract	0.260	0.000	0.262
INSPEcT_diffsteady-class	2.408	0.024	2.430
chisqmodel	0.068	0.004	0.073
chisqtest	0.008	0.000	0.007
combine	0.264	0.028	0.292
compareSteady	7.368	0.160	7.576
geneClass	0.124	0.000	0.126
getModel	0.008	0.000	0.007
inHeatmap	0.160	0.000	0.161
labeledSF	0.000	0.004	0.007
logLik	0.008	0.000	0.008
makeModelRates	0.524	0.004	0.528
makeRPKMs	5.688	0.132	7.715
makeSimDataset	7.436	0.256	13.161
makeSimModel	6.284	0.260	12.190
modelRates	28.100	0.036	28.157
modelingParams	0.016	0.000	0.013
nGenes	0.008	0.000	0.006
nTpts	0.008	0.000	0.007
newINSPEcT	1.456	0.000	1.459
plotGene	0.028	0.000	0.028
plotMA	1.12	0.00	1.14
ratePvals	0.048	0.000	0.045
ratesFirstGuess	1.476	0.004	1.482
ratesFirstGuessVar	1.484	0.008	1.493
removeModel	0.056	0.000	0.057
rocCurve	1.888	0.012	1.899
rocThresholds	22.584	0.008	22.604
sfPlot	2.072	0.000	2.076
split	0.080	0.000	0.081
testingParams	0.960	0.000	0.965
totalSF	0.008	0.000	0.007
tpts	0.004	0.000	0.006
viewModelRates	0.004	0.000	0.007