BioC 3.4: CHECK report for INSPEcT on morelia

Package: INSPEcT

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.4.0.tar.gz

StartedAt: 2017-04-15 03:51:03 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 04:00:55 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 592.2 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 ... 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         39.226  0.226  39.461
rocThresholds      25.160  0.076  25.287
makeSimDataset     21.463  0.459  30.836
makeSimModel       20.374  0.387  29.828
sfPlot             15.891  0.092  16.005
ratesFirstGuessVar 14.153  0.070  14.229
newINSPEcT         12.982  0.061  13.045
ratesFirstGuess    12.168  0.067  12.236
compareSteady       9.018  0.123   9.364
makeRPKMs           4.901  0.599 153.274
* 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
** 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	0.012	0.004	0.017
Extract	0.092	0.013	0.104
INSPEcT_diffsteady-class	1.501	0.045	1.545
chisqmodel	0.030	0.010	0.058
chisqtest	0.009	0.010	0.019
combine	0.155	0.010	0.166
compareSteady	9.018	0.123	9.364
geneClass	0.040	0.009	0.049
getModel	0.010	0.010	0.021
inHeatmap	0.026	0.010	0.060
labeledSF	0.010	0.012	0.021
logLik	0.01	0.01	0.02
makeModelRates	0.513	0.023	0.536
makeRPKMs	4.901	0.599	153.274
makeSimDataset	21.463	0.459	30.836
makeSimModel	20.374	0.387	29.828
modelRates	39.226	0.226	39.461
modelingParams	0.017	0.007	0.023
nGenes	0.006	0.004	0.009
nTpts	0.006	0.003	0.009
newINSPEcT	12.982	0.061	13.045
plotGene	0.049	0.005	0.070
plotMA	0.966	0.038	1.125
ratePvals	0.039	0.010	0.050
ratesFirstGuess	12.168	0.067	12.236
ratesFirstGuessVar	14.153	0.070	14.229
removeModel	0.059	0.005	0.064
rocCurve	2.170	0.036	2.208
rocThresholds	25.160	0.076	25.287
sfPlot	15.891	0.092	16.005
split	0.080	0.013	0.094
testingParams	1.432	0.013	1.447
totalSF	0.006	0.011	0.017
tpts	0.008	0.012	0.021
viewModelRates	0.007	0.010	0.016