BioC 3.4: CHECK report for INSPEcT on zin1

Package: INSPEcT

Version: 1.3.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.3.2.tar.gz

StartedAt: 2016-09-20 08:11:26 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:17:16 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 349.9 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_1.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.2’
* 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         39.148  0.128  39.277
rocThresholds      24.512  0.072  24.586
makeSimDataset     17.948  0.896  23.288
makeSimModel       17.236  0.288  21.682
ratesFirstGuess    12.584  0.072  12.655
newINSPEcT         12.320  0.060  12.379
ratesFirstGuessVar 12.248  0.036  12.285
sfPlot             12.220  0.040  12.264
compareSteady       9.044  0.716   9.769
* 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
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	0.012	0.000	0.011
Extract	0.140	0.000	0.137
INSPEcT_diffsteady-class	1.924	0.824	2.749
chisqmodel	0.028	0.004	0.031
chisqtest	0.008	0.000	0.008
combine	0.136	0.016	0.151
compareSteady	9.044	0.716	9.769
geneClass	0.044	0.000	0.044
getModel	0.008	0.000	0.008
inHeatmap	0.032	0.004	0.036
labeledSF	0.004	0.000	0.008
logLik	0.008	0.000	0.008
makeModelRates	0.604	0.000	0.606
makeRPKMs	4.704	0.052	4.826
makeSimDataset	17.948	0.896	23.288
makeSimModel	17.236	0.288	21.682
modelRates	39.148	0.128	39.277
modelingParams	0.012	0.000	0.014
nGenes	0.008	0.000	0.007
nTpts	0.008	0.000	0.006
newINSPEcT	12.320	0.060	12.379
plotGene	0.032	0.000	0.030
plotMA	0.956	0.048	1.012
ratePvals	0.044	0.000	0.041
ratesFirstGuess	12.584	0.072	12.655
ratesFirstGuessVar	12.248	0.036	12.285
removeModel	0.040	0.004	0.043
rocCurve	2.036	0.040	2.077
rocThresholds	24.512	0.072	24.586
sfPlot	12.220	0.040	12.264
split	0.056	0.004	0.060
testingParams	1.14	0.00	1.14
totalSF	0.008	0.000	0.007
tpts	0.008	0.000	0.007
viewModelRates	0.008	0.000	0.008