BioC 3.2: CHECK report for INSPEcT on zin1

Package: INSPEcT

Version: 1.0.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.0.2.tar.gz

StartedAt: 2016-04-23 02:04:34 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:10:39 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 365.4 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_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.0.2’
* 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 ... [14s/14s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [205s/199s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         43.266  0.024  43.323
rocThresholds      26.185  0.024  26.293
makeSimModel       23.680  1.577  21.591
makeSimDataset     23.606  1.378  22.363
ratesFirstGuessVar 13.845  0.000  13.882
sfPlot             13.676  0.004  13.733
ratesFirstGuess    13.546  0.016  13.594
newINSPEcT         13.345  0.004  13.342
compareSteady       9.900  0.029   9.933
makeRPKMs           5.762  0.052   5.825
* 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: OK

* 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	0.004	0.008	0.010
Extract	0.083	0.000	0.082
INSPEcT_diffsteady-class	1.891	0.016	1.906
chisqmodel	0.03	0.00	0.03
chisqtest	0.007	0.004	0.008
combine	0.130	0.008	0.140
compareSteady	9.900	0.029	9.933
geneClass	0.039	0.004	0.043
getModel	0.004	0.000	0.008
inHeatmap	0.033	0.000	0.033
labeledSF	0.003	0.004	0.007
logLik	0.009	0.000	0.008
makeModelRates	0.910	0.000	0.927
makeRPKMs	5.762	0.052	5.825
makeSimDataset	23.606	1.378	22.363
makeSimModel	23.680	1.577	21.591
modelRates	43.266	0.024	43.323
modelingParams	0.011	0.004	0.015
nGenes	0.007	0.000	0.007
nTpts	0.007	0.000	0.007
newINSPEcT	13.345	0.004	13.342
plotGene	0.032	0.000	0.032
plotMA	1.010	0.000	1.009
ratePvals	0.040	0.004	0.044
ratesFirstGuess	13.546	0.016	13.594
ratesFirstGuessVar	13.845	0.000	13.882
removeModel	0.048	0.000	0.048
rocCurve	2.070	0.008	2.077
rocThresholds	26.185	0.024	26.293
sfPlot	13.676	0.004	13.733
split	0.075	0.000	0.075
testingParams	1.303	0.000	1.302
totalSF	0.003	0.004	0.007
tpts	0.007	0.000	0.007
viewModelRates	0.008	0.000	0.008