BioC 3.2: CHECK report for INSPEcT on oaxaca

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 04:50:00 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:56:17 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 376.7 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [16s/16s] 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 ... [364s/180s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         60.453  9.272  45.268
makeSimModel       35.806 15.802  20.168
makeSimDataset     32.338 12.922  16.588
newINSPEcT         25.817 14.578   8.966
sfPlot             24.045 10.349   8.048
rocThresholds      34.040  0.085  34.178
ratesFirstGuess    23.926  9.819   8.180
ratesFirstGuessVar 23.484  9.969   7.961
makeGtfFromDb       4.214  0.350  13.311
* 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	0.014	0.003	0.016
Extract	0.126	0.003	0.129
chisqmodel	0.057	0.003	0.060
chisqtest	0.012	0.003	0.014
combine	0.195	0.002	0.197
geneClass	0.066	0.002	0.068
getModel	0.010	0.002	0.013
inHeatmap	0.047	0.004	0.050
labeledSF	0.009	0.002	0.011
logLik	0.011	0.002	0.013
makeGtfFromDb	4.214	0.350	13.311
makeModelRates	0.875	0.053	0.954
makeRPKMs	0.003	0.000	0.004
makeSimDataset	32.338	12.922	16.588
makeSimModel	35.806	15.802	20.168
modelRates	60.453	9.272	45.268
modelingParams	0.020	0.021	0.040
nCores	0.028	0.026	0.053
nGenes	0.01	0.01	0.02
nTpts	0.010	0.011	0.021
newINSPEcT	25.817	14.578	8.966
plotGene	0.047	0.017	0.064
ratePvals	0.062	0.018	0.080
ratesFirstGuess	23.926	9.819	8.180
ratesFirstGuessVar	23.484	9.969	7.961
removeModel	0.075	0.018	0.093
rocCurve	3.581	0.157	3.745
rocThresholds	34.040	0.085	34.178
sfPlot	24.045	10.349	8.048
split	0.111	0.025	0.136
testingParams	1.750	0.060	1.812
totalSF	0.010	0.013	0.023
tpts	0.010	0.012	0.021
viewModelRates	0.011	0.011	0.021