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: 2015-10-27 09:06:10 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:13:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 432.2 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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


* 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 ... [662s/183s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
makeSimDataset     49.792 65.253  20.685
modelRates         77.856 27.497  46.808
makeSimModel       53.838 43.080  21.781
newINSPEcT         41.429 36.298   8.736
sfPlot             39.753 30.988   8.087
ratesFirstGuess    39.697 29.771   8.061
ratesFirstGuessVar 38.973 29.045   7.973
rocThresholds      34.792  0.076  34.873
makeGtfFromDb       4.748  0.295   7.348
* 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	0.005	0.018
Extract	0.110	0.008	0.118
chisqmodel	0.050	0.005	0.056
chisqtest	0.011	0.005	0.015
combine	0.181	0.005	0.185
geneClass	0.066	0.004	0.071
getModel	0.010	0.004	0.014
inHeatmap	0.049	0.006	0.055
labeledSF	0.010	0.004	0.014
logLik	0.011	0.005	0.015
makeGtfFromDb	4.748	0.295	7.348
makeModelRates	0.883	0.071	0.978
makeRPKMs	0.003	0.001	0.004
makeSimDataset	49.792	65.253	20.685
makeSimModel	53.838	43.080	21.781
modelRates	77.856	27.497	46.808
modelingParams	0.019	0.038	0.057
nCores	0.024	0.041	0.065
nGenes	0.009	0.018	0.028
nTpts	0.009	0.017	0.025
newINSPEcT	41.429	36.298	8.736
plotGene	0.053	0.036	0.089
ratePvals	0.074	0.033	0.107
ratesFirstGuess	39.697	29.771	8.061
ratesFirstGuessVar	38.973	29.045	7.973
removeModel	0.082	0.037	0.118
rocCurve	3.943	0.278	4.315
rocThresholds	34.792	0.076	34.873
sfPlot	39.753	30.988	8.087
split	0.140	0.047	0.188
testingParams	1.764	0.127	1.892
totalSF	0.009	0.017	0.026
tpts	0.009	0.017	0.027
viewModelRates	0.010	0.017	0.027