BioC 3.2: CHECK report for TCC on oaxaca

Package: TCC

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.9.2.tar.gz

StartedAt: 2015-08-24 04:20:04 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:31:28 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 684.8 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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.9.2’
* 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 ... [19s/20s] 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 ... [101s/101s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 17.894  0.075  18.070
calcAUCValue       13.430  0.059  13.550
plotFCPseudocolor  12.275  0.039  12.681
calcNormFactors    11.212  0.112  11.442
TCC-class          11.029  0.212  11.264
plot.TCC            9.062  0.120   9.288
hypoData_mg         6.386  0.020   6.443
hypoData            6.018  0.024   6.063
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [402s/406s]
 [402s/406s] 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	0.020	0.001	0.020
TCC-class	11.029	0.212	11.264
TCC	0.011	0.001	0.012
WAD	0.491	0.009	0.500
arab	0.053	0.005	0.058
calcAUCValue	13.430	0.059	13.550
calcNormFactors	11.212	0.112	11.442
clusterSample	0.084	0.002	0.087
estimateDE	1.512	0.017	1.533
filterLowCountGenes	0.029	0.001	0.031
getNormalizedData	0.303	0.010	0.312
getResult	1.945	0.026	1.973
hypoData	6.018	0.024	6.063
hypoData_mg	6.386	0.020	6.443
hypoData_ts	0.002	0.000	0.003
nakai	0.042	0.003	0.045
plot.TCC	9.062	0.120	9.288
plotFCPseudocolor	12.275	0.039	12.681
simulateReadCounts	17.894	0.075	18.070