Package: INSPEcT

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings INSPEcT_1.10.0.tar.gz

StartedAt: 2018-10-16 22:05:26 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:11:41 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 375.3 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 --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings INSPEcT_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/INSPEcT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
modelRates     39.533  0.221  39.978
rocThresholds  33.012  0.162  33.332
compareSteady   9.102  0.283   9.468
makeSimDataset  8.532  0.840   9.074
makeSimModel    8.330  0.830   8.858
makeRPKMs       6.061  0.485   7.127
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL INSPEcT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘INSPEcT’ ...
** R
** data
** inst
** byte-compile and prepare 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	0.014	0.003	0.019
Extract	0.149	0.015	0.168
INSPEcT_diffsteady-class	2.301	0.095	2.422
chisqmodel	0.032	0.024	0.056
chisqtest	0.009	0.023	0.032
combine	0.188	0.026	0.219
compareSteady	9.102	0.283	9.468
geneClass	0.043	0.023	0.066
getModel	0.008	0.022	0.030
inHeatmap	0.060	0.024	0.085
labeledSF	0.009	0.025	0.039
logLik	0.008	0.023	0.031
makeModelRates	0.789	0.060	0.856
makeRPKMs	6.061	0.485	7.127
makeSimDataset	8.532	0.840	9.074
makeSimModel	8.330	0.830	8.858
modelRates	39.533	0.221	39.978
modelingParams	0.016	0.010	0.025
nGenes	0.011	0.009	0.021
nTpts	0.011	0.009	0.020
newINSPEcT	2.279	0.042	2.341
plotGene	0.035	0.005	0.041
plotMA	1.504	0.066	1.582
ratePvals	0.053	0.001	0.057
ratesFirstGuess	2.219	0.064	2.295
ratesFirstGuessVar	2.215	0.020	2.245
removeModel	0.044	0.001	0.045
rocCurve	2.818	0.067	2.901
rocThresholds	33.012	0.162	33.332
sfPlot	2.126	0.022	2.167
split	0.058	0.004	0.062
testingParams	1.302	0.005	1.316
totalSF	0.007	0.003	0.011
tpts	0.011	0.004	0.015
viewModelRates	0.013	0.003	0.016