BioC 3.5: CHECK report for TCC on veracruz2

Package: TCC

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.16.0.tar.gz

StartedAt: 2017-10-18 09:37:06 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:48:04 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 657.9 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TCC.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 ‘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
simulateReadCounts 14.998  0.151  18.859
calcAUCValue       11.576  0.128  13.845
TCC-class          10.250  0.299  10.865
plotFCPseudocolor   9.372  0.090  11.275
calcNormFactors     8.505  0.122  10.120
plot.TCC            7.977  0.190  10.473
hypoData_mg         5.316  0.052   6.857
hypoData            4.879  0.043   6.283
* 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	0.066	0.002	0.069
TCC-class	10.250	0.299	10.865
TCC	0.009	0.002	0.012
WAD	0.191	0.007	0.199
arab	0.043	0.006	0.049
calcAUCValue	11.576	0.128	13.845
calcNormFactors	8.505	0.122	10.120
clusterSample	0.095	0.008	0.136
estimateDE	1.451	0.014	1.921
filterLowCountGenes	0.075	0.003	0.101
getNormalizedData	0.323	0.005	0.393
getResult	1.874	0.017	2.375
hypoData	4.879	0.043	6.283
hypoData_mg	5.316	0.052	6.857
hypoData_ts	0.002	0.002	0.004
makeFCMatrix	0.004	0.000	0.005
nakai	0.039	0.003	0.053
plot.TCC	7.977	0.190	10.473
plotFCPseudocolor	9.372	0.090	11.275
simulateReadCounts	14.998	0.151	18.859