BioC 3.4: CHECK report for INSPEcT on morelia

Package: INSPEcT

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.3.2.tar.gz

StartedAt: 2016-09-20 08:09:46 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:15:19 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 333.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: INSPEcT.Rcheck

Warnings: 1

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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_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.2’
* 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 ... OK
* checking installed package size ... OK
* 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'INSPEcT,ANY,ANY,ANY'
  generic '[' and siglist 'INSPEcT_model,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         33.822  0.172  33.995
rocThresholds      20.705  0.071  20.779
makeSimDataset     16.244  0.363  21.431
makeSimModel       16.143  0.356  21.599
ratesFirstGuess    12.107  0.077  12.185
newINSPEcT         11.874  0.051  11.925
ratesFirstGuessVar 11.747  0.048  11.795
sfPlot             11.536  0.058  11.594
compareSteady       7.683  0.090   7.866
makeRPKMs           3.535  0.395  17.144
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.

* installing *source* package ‘INSPEcT’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘split’ from package ‘base’ in package ‘INSPEcT’
Creating a generic function for ‘AIC’ from package ‘stats’ in package ‘INSPEcT’
** 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	0.008	0.003	0.011
Extract	0.106	0.003	0.109
INSPEcT_diffsteady-class	1.560	0.043	1.602
chisqmodel	0.024	0.009	0.034
chisqtest	0.006	0.008	0.016
combine	0.113	0.019	0.131
compareSteady	7.683	0.090	7.866
geneClass	0.036	0.010	0.045
getModel	0.006	0.009	0.015
inHeatmap	0.028	0.010	0.039
labeledSF	0.007	0.010	0.017
logLik	0.007	0.011	0.018
makeModelRates	0.485	0.022	0.506
makeRPKMs	3.535	0.395	17.144
makeSimDataset	16.244	0.363	21.431
makeSimModel	16.143	0.356	21.599
modelRates	33.822	0.172	33.995
modelingParams	0.012	0.004	0.016
nGenes	0.006	0.002	0.007
nTpts	0.005	0.002	0.008
newINSPEcT	11.874	0.051	11.925
plotGene	0.028	0.004	0.031
plotMA	0.880	0.036	0.917
ratePvals	0.038	0.007	0.046
ratesFirstGuess	12.107	0.077	12.185
ratesFirstGuessVar	11.747	0.048	11.795
removeModel	0.039	0.002	0.041
rocCurve	1.873	0.031	1.904
rocThresholds	20.705	0.071	20.779
sfPlot	11.536	0.058	11.594
split	0.054	0.009	0.063
testingParams	0.969	0.009	0.978
totalSF	0.006	0.008	0.015
tpts	0.005	0.009	0.014
viewModelRates	0.007	0.009	0.016