BioC 3.5: CHECK report for INSPEcT on malbec2

Package: INSPEcT

Version: 1.6.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.6.1.tar.gz

StartedAt: 2017-08-15 23:58:22 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-16 00:03:28 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 305.5 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/INSPEcT.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.6.1’
* 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 ... 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 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     25.832  0.064  25.914
rocThresholds  21.536  0.128  21.675
makeSimDataset  8.048  0.300  13.731
compareSteady   6.764  0.228   7.014
makeSimModel    5.980  0.300  11.803
makeRPKMs       5.156  0.156  15.976
* 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
** 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	0.010
Extract	0.188	0.000	0.189
INSPEcT_diffsteady-class	2.492	0.068	2.564
chisqmodel	0.064	0.004	0.070
chisqtest	0.008	0.000	0.008
combine	0.252	0.016	0.267
compareSteady	6.764	0.228	7.014
geneClass	0.116	0.004	0.121
getModel	0.004	0.000	0.007
inHeatmap	0.236	0.000	0.239
labeledSF	0.008	0.000	0.012
logLik	0.012	0.000	0.012
makeModelRates	0.584	0.004	0.588
makeRPKMs	5.156	0.156	15.976
makeSimDataset	8.048	0.300	13.731
makeSimModel	5.980	0.300	11.803
modelRates	25.832	0.064	25.914
modelingParams	0.020	0.004	0.024
nGenes	0.012	0.000	0.011
nTpts	0.012	0.000	0.008
newINSPEcT	1.640	0.016	1.656
plotGene	0.028	0.000	0.028
plotMA	1.188	0.084	1.289
ratePvals	0.052	0.000	0.052
ratesFirstGuess	2.028	0.012	2.040
ratesFirstGuessVar	1.468	0.008	1.476
removeModel	0.052	0.004	0.056
rocCurve	1.876	0.104	1.985
rocThresholds	21.536	0.128	21.675
sfPlot	1.584	0.008	1.594
split	0.048	0.004	0.051
testingParams	0.892	0.000	0.892
totalSF	0.008	0.000	0.007
tpts	0.008	0.000	0.006
viewModelRates	0.008	0.000	0.007