BioC 3.2: CHECK report for INSPEcT on oaxaca

Package: INSPEcT

Version: 0.99.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_0.99.8.tar.gz

StartedAt: 2015-08-24 00:59:49 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:07:12 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 443.9 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_0.99.8.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 ‘0.99.8’
* 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 ... [15s/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 ... [375s/218s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         63.538 10.824  49.313
makeSimModel       35.549 13.706  20.855
makeSimDataset     33.678 13.138  19.184
ratesFirstGuess    25.745 13.652  10.124
rocThresholds      38.009  0.161  39.015
ratesFirstGuessVar 25.190 12.326   9.053
sfPlot             24.041 11.321   8.735
newINSPEcT         24.006 10.221   8.535
makeGtfFromDb       1.388  0.376  34.153
* 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	0.015	0.004	0.046
Extract	0.134	0.003	0.137
chisqmodel	0.056	0.005	0.061
chisqtest	0.013	0.004	0.017
combine	0.214	0.004	0.219
geneClass	0.072	0.004	0.077
getModel	0.012	0.004	0.015
inHeatmap	0.051	0.004	0.089
labeledSF	0.011	0.003	0.015
logLik	0.012	0.004	0.016
makeGtfFromDb	1.388	0.376	34.153
makeModelRates	1.266	0.035	1.358
makeRPKMs	0.004	0.000	0.003
makeSimDataset	33.678	13.138	19.184
makeSimModel	35.549	13.706	20.855
modelRates	63.538	10.824	49.313
modelingParams	0.022	0.006	0.029
nCores	0.031	0.014	0.044
nGenes	0.011	0.003	0.014
nTpts	0.011	0.003	0.014
newINSPEcT	24.006	10.221	8.535
plotGene	0.053	0.013	0.089
ratePvals	0.071	0.010	0.083
ratesFirstGuess	25.745	13.652	10.124
ratesFirstGuessVar	25.190	12.326	9.053
removeModel	0.084	0.012	0.096
rocCurve	3.417	0.123	3.630
rocThresholds	38.009	0.161	39.015
sfPlot	24.041	11.321	8.735
split	0.112	0.023	0.137
testingParams	1.854	0.077	1.978
totalSF	0.011	0.011	0.023
tpts	0.011	0.011	0.024
viewModelRates	0.012	0.012	0.027