BioC 3.2: CHECK report for INSPEcT on oaxaca

Package: INSPEcT

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.0.2.tar.gz

StartedAt: 2016-04-23 01:22:07 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:30:44 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 517.1 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.0.2’
* 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 ... [19s/20s] 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 ... [286s/290s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         56.011  0.160  56.461
makeSimDataset     35.720  7.392  29.486
makeSimModel       34.200  6.496  29.183
rocThresholds      32.626  0.098  33.151
sfPlot             19.599  0.051  19.801
ratesFirstGuessVar 19.096  0.038  19.251
newINSPEcT         18.642  0.034  18.759
ratesFirstGuess    16.596  0.056  16.854
compareSteady      11.670  0.093  12.070
makeRPKMs           6.617  0.513  31.227
* 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	0.013	0.003	0.016
Extract	0.126	0.004	0.130
INSPEcT_diffsteady-class	1.893	0.055	1.952
chisqmodel	0.039	0.011	0.075
chisqtest	0.008	0.009	0.047
combine	0.125	0.024	0.165
compareSteady	11.670	0.093	12.070
geneClass	0.058	0.012	0.071
getModel	0.009	0.012	0.020
inHeatmap	0.041	0.014	0.055
labeledSF	0.010	0.012	0.022
logLik	0.012	0.013	0.024
makeModelRates	1.127	0.032	1.160
makeRPKMs	6.617	0.513	31.227
makeSimDataset	35.720	7.392	29.486
makeSimModel	34.200	6.496	29.183
modelRates	56.011	0.160	56.461
modelingParams	0.018	0.003	0.021
nGenes	0.010	0.003	0.012
nTpts	0.010	0.002	0.011
newINSPEcT	18.642	0.034	18.759
plotGene	0.045	0.002	0.158
plotMA	1.204	0.056	3.598
ratePvals	0.048	0.009	0.070
ratesFirstGuess	16.596	0.056	16.854
ratesFirstGuessVar	19.096	0.038	19.251
removeModel	0.064	0.007	0.071
rocCurve	2.296	0.052	2.698
rocThresholds	32.626	0.098	33.151
sfPlot	19.599	0.051	19.801
split	0.110	0.012	0.123
testingParams	1.714	0.015	1.761
totalSF	0.009	0.015	0.025
tpts	0.010	0.016	0.025
viewModelRates	0.010	0.015	0.025