Package: INSPEcT

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.8.0.tar.gz

StartedAt: 2018-04-12 05:15:49 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:21:53 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 364.1 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/INSPEcT.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’
* 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 ‘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 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
modelRates     38.019  0.198  38.782
rocThresholds  30.444  0.130  31.163
makeSimDataset  9.616  0.528  10.444
compareSteady   8.835  0.180   9.165
makeSimModel    8.135  0.465   8.841
makeRPKMs       6.327  0.254   6.685
* 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	0.011	0.001	0.017
Extract	0.158	0.005	0.164
INSPEcT_diffsteady-class	2.330	0.084	2.445
chisqmodel	0.452	0.027	0.489
chisqtest	0.010	0.004	0.017
combine	0.376	0.028	0.410
compareSteady	8.835	0.180	9.165
geneClass	0.174	0.019	0.196
getModel	0.006	0.021	0.028
inHeatmap	0.216	0.023	0.242
labeledSF	0.009	0.019	0.029
logLik	0.010	0.020	0.029
makeModelRates	0.751	0.042	0.813
makeRPKMs	6.327	0.254	6.685
makeSimDataset	9.616	0.528	10.444
makeSimModel	8.135	0.465	8.841
modelRates	38.019	0.198	38.782
modelingParams	0.018	0.039	0.057
nGenes	0.009	0.020	0.029
nTpts	0.009	0.020	0.029
newINSPEcT	2.443	0.051	2.523
plotGene	0.030	0.002	0.032
plotMA	1.548	0.078	1.647
ratePvals	0.061	0.020	0.082
ratesFirstGuess	2.049	0.054	2.130
ratesFirstGuessVar	1.995	0.020	2.041
removeModel	0.073	0.004	0.082
rocCurve	2.674	0.071	2.791
rocThresholds	30.444	0.130	31.163
sfPlot	2.055	0.034	2.145
split	0.064	0.024	0.087
testingParams	1.332	0.023	1.369
totalSF	0.007	0.019	0.026
tpts	0.010	0.021	0.032
viewModelRates	0.010	0.019	0.029