BioC 3.6: CHECK report for INSPEcT on veracruz1

Package: INSPEcT

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.7.1.tar.gz

StartedAt: 2017-08-16 04:33:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:38:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 320.8 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_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.7.1’
* 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     33.190  0.134  34.247
rocThresholds  24.717  0.106  25.391
makeSimDataset  7.897  0.385   8.538
compareSteady   7.724  0.112   8.038
makeSimModel    6.779  0.394   7.468
makeRPKMs       5.333  0.339   6.284
* 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	0.003	0.012
Extract	0.177	0.004	0.184
INSPEcT_diffsteady-class	2.397	0.069	2.518
chisqmodel	0.078	0.024	0.102
chisqtest	0.008	0.019	0.029
combine	0.318	0.070	0.408
compareSteady	7.724	0.112	8.038
geneClass	0.160	0.019	0.185
getModel	0.006	0.021	0.028
inHeatmap	0.186	0.022	0.210
labeledSF	0.007	0.020	0.026
logLik	0.006	0.017	0.023
makeModelRates	0.733	0.040	0.807
makeRPKMs	5.333	0.339	6.284
makeSimDataset	7.897	0.385	8.538
makeSimModel	6.779	0.394	7.468
modelRates	33.190	0.134	34.247
modelingParams	0.014	0.005	0.019
nGenes	0.009	0.003	0.011
nTpts	0.006	0.002	0.009
newINSPEcT	1.779	0.017	1.870
plotGene	0.027	0.002	0.035
plotMA	1.278	0.068	1.394
ratePvals	0.075	0.030	0.105
ratesFirstGuess	1.802	0.027	1.886
ratesFirstGuessVar	1.795	0.014	1.866
removeModel	0.071	0.002	0.082
rocCurve	2.741	0.058	2.886
rocThresholds	24.717	0.106	25.391
sfPlot	1.611	0.011	1.676
split	0.049	0.001	0.050
testingParams	1.023	0.005	1.066
totalSF	0.005	0.001	0.007
tpts	0.005	0.002	0.007
viewModelRates	0.006	0.002	0.008