BioC 3.4: CHECK report for TCC on morelia

Package: TCC

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.13.1.tar.gz

StartedAt: 2016-09-20 13:47:07 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:55:13 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 486.1 seconds

RetCode: 0

Status:  OK

CheckDir: TCC.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 TCC_1.13.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TCC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCC’ version ‘1.13.1’
* 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 ‘TCC’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calcAUCValue       11.435  0.096  11.642
TCC-class          11.201  0.277  11.542
simulateReadCounts 10.372  0.066  10.468
plot.TCC            9.985  0.211  10.320
calcNormFactors     9.250  0.123   9.421
plotFCPseudocolor   6.463  0.053   6.665
hypoData            5.109  0.041   5.192
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 ‘TCC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘calcNormFactors’ in package ‘TCC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCC)

name	user	system	elapsed
ROKU	0.037	0.005	0.042
TCC-class	11.201	0.277	11.542
TCC	0.016	0.002	0.019
WAD	0.628	0.013	0.642
arab	0.049	0.007	0.056
calcAUCValue	11.435	0.096	11.642
calcNormFactors	9.250	0.123	9.421
clusterSample	0.076	0.006	0.082
estimateDE	1.591	0.008	1.615
filterLowCountGenes	0.031	0.003	0.034
getNormalizedData	0.349	0.010	0.360
getResult	1.885	0.010	1.914
hypoData	5.109	0.041	5.192
hypoData_mg	4.622	0.033	4.671
hypoData_ts	0.002	0.002	0.004
makeFCMatrix	0.005	0.000	0.005
nakai	0.055	0.004	0.059
plot.TCC	9.985	0.211	10.320
plotFCPseudocolor	6.463	0.053	6.665
simulateReadCounts	10.372	0.066	10.468