BioC 3.2: CHECK report for INSPEcT on linux1.bioconductor.org

Package: INSPEcT

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.0.0.tar.gz

StartedAt: 2015-10-27 04:52:10 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:57:42 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 331.6 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [14s/14s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [317s/159s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         52.259 11.320  41.650
makeSimModel       29.321 19.191  21.954
makeSimDataset     26.012 13.271  16.252
newINSPEcT         20.273 12.411   9.078
ratesFirstGuess    19.312 11.033   8.904
ratesFirstGuessVar 18.477 11.196   8.982
sfPlot             18.633 10.630   8.394
rocThresholds      25.682  0.007  25.705
* 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
  ‘/home/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	0.011	0.004	0.015
Extract	0.114	0.004	0.118
chisqmodel	0.053	0.000	0.053
chisqtest	0.012	0.000	0.012
combine	0.177	0.000	0.177
geneClass	0.069	0.000	0.070
getModel	0.011	0.000	0.011
inHeatmap	0.05	0.00	0.05
labeledSF	0.011	0.000	0.010
logLik	0.009	0.004	0.013
makeGtfFromDb	3.280	0.048	3.332
makeModelRates	0.633	0.028	0.666
makeRPKMs	0.002	0.000	0.002
makeSimDataset	26.012	13.271	16.252
makeSimModel	29.321	19.191	21.954
modelRates	52.259	11.320	41.650
modelingParams	0.016	0.000	0.013
nCores	0.015	0.024	0.046
nGenes	0.007	0.000	0.007
nTpts	0.006	0.000	0.006
newINSPEcT	20.273	12.411	9.078
plotGene	0.029	0.003	0.034
ratePvals	0.044	0.000	0.043
ratesFirstGuess	19.312	11.033	8.904
ratesFirstGuessVar	18.477	11.196	8.982
removeModel	0.069	0.004	0.072
rocCurve	3.780	0.086	3.867
rocThresholds	25.682	0.007	25.705
sfPlot	18.633	10.630	8.394
split	0.108	0.003	0.112
testingParams	1.196	0.012	1.219
totalSF	0.007	0.000	0.007
tpts	0.006	0.000	0.006
viewModelRates	0.006	0.000	0.007