BioC 3.5: CHECK report for INSPEcT on toluca2

Package: INSPEcT

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.5.5.tar.gz

StartedAt: 2017-04-23 05:31:34 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:38:28 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 414.4 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.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 INSPEcT_1.5.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.5’
* 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     48.708  0.196  49.400
rocThresholds  38.528  0.132  38.970
makeSimDataset 11.121  0.615  18.473
makeSimModel    9.566  0.593  17.630
compareSteady   9.667  0.131   9.816
makeRPKMs       6.749  0.440   7.664
* 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	0.010	0.005	0.015
Extract	0.170	0.006	0.176
INSPEcT_diffsteady-class	2.641	0.078	2.725
chisqmodel	0.100	0.017	0.117
chisqtest	0.010	0.015	0.024
combine	0.395	0.066	0.461
compareSteady	9.667	0.131	9.816
geneClass	0.191	0.016	0.206
getModel	0.009	0.015	0.024
inHeatmap	0.242	0.018	0.262
labeledSF	0.009	0.017	0.026
logLik	0.011	0.017	0.028
makeModelRates	0.961	0.038	1.001
makeRPKMs	6.749	0.440	7.664
makeSimDataset	11.121	0.615	18.473
makeSimModel	9.566	0.593	17.630
modelRates	48.708	0.196	49.400
modelingParams	0.017	0.007	0.024
nGenes	0.009	0.004	0.014
nTpts	0.008	0.005	0.012
newINSPEcT	2.622	0.020	2.652
plotGene	0.040	0.005	0.044
plotMA	1.634	0.080	1.742
ratePvals	0.075	0.016	0.091
ratesFirstGuess	2.624	0.055	2.689
ratesFirstGuessVar	2.683	0.021	2.718
removeModel	0.091	0.003	0.096
rocCurve	3.753	0.079	3.890
rocThresholds	38.528	0.132	38.970
sfPlot	2.786	0.023	2.829
split	0.080	0.005	0.089
testingParams	1.696	0.008	1.717
totalSF	0.009	0.004	0.013
tpts	0.009	0.004	0.013
viewModelRates	0.010	0.004	0.013