BioC 3.2: CHECK report for INSPEcT on perceval

Package: INSPEcT

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.0.0.tar.gz

StartedAt: 2015-11-10 06:09:26 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:16:36 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 430.5 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* 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 ... [22s/22s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
* 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 ... [717s/190s] OK
Examples with CPU or elapsed time > 5s
                     user  system elapsed
sfPlot             41.397 132.628  17.667
modelRates         76.927  27.137  45.714
makeSimModel       52.984  40.684  21.388
makeSimDataset     48.377  34.516  16.872
ratesFirstGuess    39.404  28.731   7.812
newINSPEcT         39.070  29.013   7.802
ratesFirstGuessVar 38.768  28.334   7.623
rocThresholds      34.459   0.125  34.587
makeGtfFromDb       4.749   0.441  11.919
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.

* 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	0.013	0.004	0.016
Extract	0.115	0.005	0.122
chisqmodel	0.052	0.004	0.055
chisqtest	0.011	0.003	0.014
combine	0.176	0.004	0.180
geneClass	0.065	0.003	0.068
getModel	0.010	0.003	0.012
inHeatmap	0.047	0.004	0.051
labeledSF	0.009	0.003	0.013
logLik	0.010	0.003	0.013
makeGtfFromDb	4.749	0.441	11.919
makeModelRates	0.874	0.069	0.963
makeRPKMs	0.003	0.000	0.003
makeSimDataset	48.377	34.516	16.872
makeSimModel	52.984	40.684	21.388
modelRates	76.927	27.137	45.714
modelingParams	0.019	0.040	0.059
nCores	0.023	0.044	0.066
nGenes	0.009	0.019	0.028
nTpts	0.009	0.019	0.028
newINSPEcT	39.070	29.013	7.802
plotGene	0.052	0.034	0.087
ratePvals	0.073	0.033	0.106
ratesFirstGuess	39.404	28.731	7.812
ratesFirstGuessVar	38.768	28.334	7.623
removeModel	0.08	0.04	0.12
rocCurve	3.910	0.325	4.236
rocThresholds	34.459	0.125	34.587
sfPlot	41.397	132.628	17.667
split	0.126	0.045	0.171
testingParams	1.733	0.128	1.860
totalSF	0.009	0.017	0.026
tpts	0.009	0.016	0.026
viewModelRates	0.010	0.017	0.027