BioC 3.4: CHECK report for INSPEcT on malbec1

Package: INSPEcT

Version: 1.4.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.4.0.tar.gz

StartedAt: 2017-04-14 23:19:16 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:25:00 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 344.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: INSPEcT.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 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         35.036  0.088  35.141
rocThresholds      21.596  0.016  21.625
makeSimDataset     15.640  0.244  20.818
makeSimModel       15.056  0.228  20.089
ratesFirstGuessVar 11.804  0.060  11.873
sfPlot             11.400  0.036  11.441
newINSPEcT         11.384  0.048  11.442
ratesFirstGuess    10.908  0.028  10.944
compareSteady       7.560  0.044   7.832
* 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
  ‘/home/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	0.008	0.000	0.008
Extract	0.076	0.008	0.083
INSPEcT_diffsteady-class	1.740	0.008	1.747
chisqmodel	0.028	0.000	0.026
chisqtest	0.008	0.000	0.008
combine	0.120	0.004	0.124
compareSteady	7.560	0.044	7.832
geneClass	0.028	0.004	0.035
getModel	0.004	0.000	0.007
inHeatmap	0.028	0.000	0.030
labeledSF	0.008	0.000	0.006
logLik	0.008	0.000	0.008
makeModelRates	0.484	0.000	0.483
makeRPKMs	4.780	0.048	4.833
makeSimDataset	15.640	0.244	20.818
makeSimModel	15.056	0.228	20.089
modelRates	35.036	0.088	35.141
modelingParams	0.008	0.004	0.013
nGenes	0.004	0.000	0.007
nTpts	0.008	0.000	0.007
newINSPEcT	11.384	0.048	11.442
plotGene	0.028	0.000	0.027
plotMA	0.888	0.000	0.888
ratePvals	0.040	0.004	0.041
ratesFirstGuess	10.908	0.028	10.944
ratesFirstGuessVar	11.804	0.060	11.873
removeModel	0.064	0.000	0.061
rocCurve	2.160	0.004	2.164
rocThresholds	21.596	0.016	21.625
sfPlot	11.400	0.036	11.441
split	0.060	0.000	0.058
testingParams	1.160	0.000	1.162
totalSF	0.012	0.000	0.012
tpts	0.012	0.000	0.012
viewModelRates	0.012	0.000	0.013