BioC 3.5: CHECK report for INSPEcT on veracruz2

Package: INSPEcT

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.6.1.tar.gz

StartedAt: 2017-08-16 04:17:54 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:23:29 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 334.9 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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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_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/INSPEcT.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.1’
* 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 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     32.583  0.138  33.617
rocThresholds  25.138  0.112  25.843
makeSimDataset  8.495  0.510  16.052
compareSteady   7.570  0.112   7.873
makeSimModel    6.479  0.413  14.252
makeRPKMs       4.977  0.213   5.338
* 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	0.010	0.002	0.012
Extract	0.122	0.004	0.127
INSPEcT_diffsteady-class	1.872	0.065	2.024
chisqmodel	0.067	0.022	0.093
chisqtest	0.008	0.017	0.028
combine	0.296	0.059	0.368
compareSteady	7.570	0.112	7.873
geneClass	0.158	0.017	0.183
getModel	0.006	0.016	0.022
inHeatmap	0.185	0.019	0.204
labeledSF	0.006	0.017	0.023
logLik	0.007	0.019	0.026
makeModelRates	0.571	0.038	0.618
makeRPKMs	4.977	0.213	5.338
makeSimDataset	8.495	0.510	16.052
makeSimModel	6.479	0.413	14.252
modelRates	32.583	0.138	33.617
modelingParams	0.017	0.007	0.022
nGenes	0.009	0.004	0.012
nTpts	0.005	0.002	0.007
newINSPEcT	1.760	0.014	1.820
plotGene	0.060	0.004	0.067
plotMA	1.321	0.081	1.452
ratePvals	0.066	0.002	0.074
ratesFirstGuess	1.883	0.033	1.950
ratesFirstGuessVar	1.864	0.013	1.966
removeModel	0.084	0.003	0.087
rocCurve	2.807	0.060	2.953
rocThresholds	25.138	0.112	25.843
sfPlot	1.811	0.012	1.861
split	0.060	0.003	0.063
testingParams	1.126	0.003	1.149
totalSF	0.008	0.002	0.010
tpts	0.009	0.003	0.011
viewModelRates	0.007	0.002	0.009