BioC 2.14: CHECK report for TCC on petty

Package: TCC

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TCC_1.4.0.tar.gz

StartedAt: 2014-10-08 00:25:02 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:44:58 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 1195.6 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 --no-multiarch TCC_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/TCC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ... [34s/34s] 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 ... [222s/225s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 42.389  0.159  43.036
calcAUCValue       30.563  0.114  30.797
plotFCPseudocolor  28.183  0.107  29.746
TCC-class          25.600  0.295  26.089
calcNormFactors    22.608  0.086  22.799
plot.TCC           20.413  0.177  20.867
hypoData           14.113  0.036  14.248
hypoData_mg        13.725  0.047  13.802
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [11m/11m]
 [11m/11m] 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

* 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
MAplot	0.002	0.000	0.001
NB	0.000	0.000	0.001
ROKU	0.076	0.003	0.083
TCC-class	25.600	0.295	26.089
TCC	0.020	0.001	0.022
WAD	0.470	0.010	0.485
arab	0.074	0.011	0.090
calcAUCValue	30.563	0.114	30.797
calcNormFactors	22.608	0.086	22.799
clusterSample	0.141	0.004	0.146
do_TbT	0.001	0.000	0.001
estimateDE	2.760	0.009	2.808
exactTestafterTbT	0.001	0.000	0.001
filterLowCountGenes	0.053	0.002	0.054
getNormalizedData	0.573	0.003	0.579
getResult	3.667	0.010	3.698
hypoData	14.113	0.036	14.248
hypoData_mg	13.725	0.047	13.802
hypoData_ts	0.003	0.001	0.004
nakai	0.065	0.004	0.069
plot.TCC	20.413	0.177	20.867
plotFCPseudocolor	28.183	0.107	29.746
simulateReadCounts	42.389	0.159	43.036