BioC 3.3: CHECK report for INSPEcT on oaxaca

Package: INSPEcT

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.2.2.tar.gz

StartedAt: 2016-10-13 02:53:38 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:01:09 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 451.4 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_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.2’
* 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         50.105  0.243  50.398
rocThresholds      27.887  0.102  28.042
makeSimDataset     23.771  0.532  29.073
makeSimModel       22.240  0.516  27.315
ratesFirstGuessVar 18.054  0.111  18.179
newINSPEcT         18.046  0.106  18.647
sfPlot             17.719  0.093  19.160
ratesFirstGuess    17.349  0.121  17.484
compareSteady      10.339  0.117  10.630
makeRPKMs           5.503  0.479  31.367
* 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
Creating a generic function for ‘split’ from package ‘base’ in package ‘INSPEcT’
Creating a generic function for ‘AIC’ from package ‘stats’ in package ‘INSPEcT’
** 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	0.009	0.002	0.010
Extract	0.092	0.003	0.094
INSPEcT_diffsteady-class	2.065	0.050	2.117
chisqmodel	0.031	0.010	0.041
chisqtest	0.010	0.010	0.019
combine	0.152	0.023	0.175
compareSteady	10.339	0.117	10.630
geneClass	0.056	0.011	0.068
getModel	0.007	0.011	0.019
inHeatmap	0.046	0.011	0.155
labeledSF	0.009	0.010	0.019
logLik	0.011	0.012	0.023
makeModelRates	0.684	0.029	0.713
makeRPKMs	5.503	0.479	31.367
makeSimDataset	23.771	0.532	29.073
makeSimModel	22.240	0.516	27.315
modelRates	50.105	0.243	50.398
modelingParams	0.019	0.005	0.024
nGenes	0.009	0.003	0.012
nTpts	0.010	0.003	0.013
newINSPEcT	18.046	0.106	18.647
plotGene	0.041	0.005	0.046
plotMA	1.166	0.054	1.220
ratePvals	0.060	0.015	0.075
ratesFirstGuess	17.349	0.121	17.484
ratesFirstGuessVar	18.054	0.111	18.179
removeModel	0.065	0.012	0.076
rocCurve	2.926	0.044	2.973
rocThresholds	27.887	0.102	28.042
sfPlot	17.719	0.093	19.160
split	0.075	0.003	0.077
testingParams	1.485	0.004	1.489
totalSF	0.007	0.003	0.009
tpts	0.010	0.002	0.012
viewModelRates	0.006	0.001	0.007