BioC 3.3: CHECK report for INSPEcT on morelia

Package: INSPEcT

Version: 1.1.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.1.8.tar.gz

StartedAt: 2016-04-21 04:07:10 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:15:13 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 483.7 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_1.1.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.1.8’
* 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/19s] 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 ... [293s/270s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         53.621  0.330  54.238
rocThresholds      32.529  0.108  32.813
makeSimDataset     25.180  0.475  32.004
makeSimModel       23.495  0.457  30.378
newINSPEcT         18.535  0.090  18.680
ratesFirstGuess    18.162  0.153  18.364
ratesFirstGuessVar 17.820  0.084  17.947
sfPlot             17.498  0.086  17.645
compareSteady      11.212  0.134  11.410
makeRPKMs           4.796  0.499  18.948
* 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	0.012	0.004	0.016
Extract	0.111	0.005	0.116
INSPEcT_diffsteady-class	2.139	0.062	2.209
chisqmodel	0.033	0.013	0.046
chisqtest	0.011	0.012	0.024
combine	0.164	0.024	0.188
compareSteady	11.212	0.134	11.410
geneClass	0.054	0.012	0.067
getModel	0.009	0.013	0.022
inHeatmap	0.034	0.013	0.047
labeledSF	0.009	0.013	0.022
logLik	0.010	0.012	0.022
makeModelRates	0.753	0.032	0.786
makeRPKMs	4.796	0.499	18.948
makeSimDataset	25.180	0.475	32.004
makeSimModel	23.495	0.457	30.378
modelRates	53.621	0.330	54.238
modelingParams	0.020	0.007	0.028
nGenes	0.010	0.004	0.014
nTpts	0.006	0.004	0.010
newINSPEcT	18.535	0.090	18.680
plotGene	0.037	0.004	0.042
plotMA	1.294	0.053	1.348
ratePvals	0.059	0.010	0.070
ratesFirstGuess	18.162	0.153	18.364
ratesFirstGuessVar	17.820	0.084	17.947
removeModel	0.064	0.003	0.067
rocCurve	2.954	0.049	3.023
rocThresholds	32.529	0.108	32.813
sfPlot	17.498	0.086	17.645
split	0.096	0.012	0.107
testingParams	1.509	0.011	1.524
totalSF	0.010	0.012	0.022
tpts	0.009	0.012	0.021
viewModelRates	0.009	0.011	0.020